Well, before I go to lunch, a couple things. First off, the lack of harmony had nothing to do with magic or was only an easy excuse. Jerks and idiots will always find a reason to complain, so taking away the magic was unwise and hardly really a good course of action.
Second, all the crystals do is just simply punish everpony…guilty and innocent alike. Basically, the comic seems to indicate Twilight would punish absolutely everybody for the sins of only a couple of ponies. And in fact, it also means good ponies would suffer by the lost of their magical talents and other dangers that might not need magic per see could still put a risk on their lives.
Third, honestly Discord just seems like a bitter cranky old man in G5, not the hedonistic jerk who loves to play with others’ feathers. So cynical he fails to see the big picture: magic had nothing to do with the lack of harmony, magic is just the scapegoat to not face the fact ponies were just so nasty they’ll let petty squabbles loose everything in the process, not that again the crystal creation was a good thing to begin with. Sure, some might pull some strings here and there, but ultimately if ponies eventually choose to succumb to bad ideas, then they’ll have no one to blame but themselves.
And fourth, a lot of the problems can be tracked down to the idea that magic is the cause or solution of problems. By that token, you could argue the same about technology, some dangerous plants or animals, and so on. Is just flat out cutting corners without actually inquiring why exactly something happens.
The Unity crystals were an emergency solution as seen with the Grogar twist in G4 S9, when the original draft was discarded and had to be replaced with something new, this was followed by criticism as it automatically means that the ponies’ magic was taken away to keep them under control. This meant that this was an abuse, and it was correct from a human perspective as one must be able to do right and wrong in one’s life in a well-functioning society where one has to live together for good and bad in social interactions regardless of the differences from pony to pony.
This is another repetition of “be kind, otherwise!” for which several of the G4 human screenwriters have become notorious. It would be wise if the child welfare authorities looked at these authors’ merits for child-rearing. European counterparts even in older times when strict discipline of children was allowed were not so black and white or extreme. The Windigo problem is that the ponies are forced to be kind to each other in order not to be exterminated, and this was not fully understood until Season 6 of G4. We do not threaten our children with prohibitive consequences for them to have a good upbringing, that they must be “kind”. Fundamentally, there is something very wrong with the human effort here when Hasbro built up the MLP.
The founders of Equestria, the feudal rulers and later Celestia were thus busy with social politics to maintain the stability of Equestria and ward off the windigos, but possibly because wise people like Starswirl may have discovered the real problem. That’s why there was so much that seemed greatly exaggerated about harmony, social cohesion, political stability etc, - when Celestia and Luna came, they had become gathering objects for the united pony tribes, a symbol of the community that was understood very early in G4. The alicorns became very important in keeping the horrors away. But they couldn’t start over, the past casting strong shadows over Equestria. This characterized much of the G4, and partly the G5.
That may be why the ponies find it so easy to return to prejudice when they forget themselves, individually they can live together, but as a collective they have not moved on from the shadows of the caste system. As the historical legacy has been “erased” in the G5, the ponies now have a very large opportunity to progress in contrast to the G4, because they started again on equal footing. This is what the “Shadowy alicorn” threatens, and which Sunny will protect at all costs, the past should be put to rest. The unicorns, the pegasi and the earth ponies may have the opportunity to break with the past, they are on equal footing when it comes to building a new society.
MYM provides a logical explanation in response to the criticism; Twilight had created the Unity Crystals and made it possible to take away the magic, it was because the pony magic had become unstable and very emotionally hypersensitive that it had become a very serious threat. A hypothesis was given as to why non-ponies had disappeared, they had come to fear the ponies which had had a very destructive effect on the magic in their surroundings. They may have chosen to flee while the ponies themselves were in great danger, the earth ponies could have been swallowed by a void while the others would have lost all magic. At the end, Sunny asked if the Unity Crystals had been put together, and it had been taken apart because the ponies’ magic had to go away. Unfortunately, it becomes another example of the “be kind, or else!” problem, and the criticism continues. At least Sunny and Zipp understood that there is coercion in practice for the ponies to be nice and do actions that they don’t really want to do.
In the IDW comics, Discord explained that Twilight wasn’t given much choice; the pony magic had gotten out of control - and since the windigos can transform magic charged with negative emotion into snow and cold - it means that the eradication of these in S9 has made the environment vulnerable to uncontrolled pony magic. Not even Discord could counter this. There was a lot of pressure on the Mane 6, the non-ponies probably couldn’t tolerate this “Nirik” problem while most of the ponies just want security and stability again. It may be possible that the ponies voluntarily give up their foci if Twilight explains to them what she can do, and the non-ponies may accept this as well. She had - that’s 100% sure - tried to make the magic neutral, but couldn’t turn off the emotional backlash from the ponies without touching the very essence of the Ponykind.
It is possible that the Unity Crystals could not be separated once all the magic was gathered in them. Yet it has happened. Criticism has not subsided after this either, it is only moved to the belief that the ponies are under a coercive regime as long as Twilight reigned, and that these lost their magic because they are again divided from each other by their prejudices. Currently I think the disagreements between the ponies were much easier to deal with as the Unity Crystals acted as a dam. The MYM episode revealed imbalance and exaggerated magic.
It is possible that the magic in G5 is much stronger than in G4 because the ponies “rebooted” after a long time of about 100 to 200 years or four pony generations. Then the effect becomes stronger, and according to the Shadowy alicorn, the magic was “unstable”, which means that all magic was not released at the end of the G5 movie. From TYT we know that the Unity Crystals are oversensitive when the ponies simply argued with each other and at the same time abused their powers to gain advantages as seen during the tournament. This would not have happened in the G4, and another proof that the magic in the G5 is too strong, too unpredictable. A lone unicorn could move a huge statue in G5 where multiple unicorns were needed for the same thing in G4.
It is possible that the magic in G5 is much stronger than in G4 because the ponies “restarted” after a long build-up of about 100 to 200 years or four pony generations. Then the effect becomes stronger, and according to the Shadowy alicorn, the magic was “unstable”, which means that all magic was not released at the end of the G5 movie. From TYT we know that the Unity Crystals are oversensitive when the ponies simply argued with each other and at the same time abused their powers to gain advantages as seen during the tournament. This would not have happened in the G4, and another proof that the magic in the G5 is too strong, too unpredictable. A lone unicorn could move a huge statue in G5 where multiple unicorns were needed for the same thing in G4.
When the Unity Crystals separated - it happened at the same time that Equestria collapsed and the whole world that Twilight and her friends had discovered in G4, had fallen apart. This does not indicate internal factors, as the ponies probably could not attack each other because MYM and TYM have shown the magic will disappear if that happens, and from TYT it happens temporarily as if the light goes out. It can happen without taking apart the Unity Crystals. Only Discord was able to separate it, but the magic didn’t go away for good. The magic continues to come to the ponies who return emotional energy in response. It was only when Discord took away the pegasus crystal that the magic disappeared for a short while. Then it means that the magic that came through the Unity Crystals is very strong. Much stronger. So if all magic were to disappear by taking apart the Unity Crystals - it is not enough to do it physically. It must happen magically too.
Then that means that it was only Twilight Sparkle who took away the magic as she created the Unity Crystals and understood how it works, and thus was able to shut it down completely. The Unity Crystals could not be separated with impunity. She knew what price had to be paid when she created the spell that could be her masterpiece, to create the Unity Crystals - and the consequences of taking away the active magic and the dangers if it returns. Which the “Shadowy alicorn” was aware of and therefore kept Maretime Bay under observation as seen in MYM. Such an action with such enormous consequences could only be defended in the worst imaginable scenarios, and it is not the uncontrolled magic of the ponies.
From the G5 movie we know that the collapse of Equestria was too recent, and from the IDW comics it suggests that a powerful external attacker was involved. An attacker that could only be stopped by taking away all active magic. It happened during a situation where everything seemed to have collapsed; Canterlot was abandoned, evacuated, the ponies isolated from each other in confusion, shock and fear, all trade stopped completely, all contact between the ponies and non-ponies was reduced to a minimum. Only the Pegasi Empire seems to have done well, but then we don’t know what has happened to eight tenths of Equestria.
Discord didn’t explain everything about why he wants to take away the magic. This is typical of him who never comes up with a complete explanation, sometimes it had to be pulled out with pliers - literally. But it is clear that he had experienced a very traumatic event, and that he had chosen to live in isolation in the ruins of Canterlot. Something very bad had happened when Equestria collapsed.