Have now read the comic. Discord came up with an evasive answer without explaining what happened to Canterlot, and explained how the Unity Crystals came into being, and why; and thus we get an insight into his motive - he wants to protect the ponies from magic, because he had seen how destructive the pony magic can be when the tribes are set against each other. And thus we encounter the big problem that was shown in the MYM special, namely that when the ponies come into conflict with each other, the magic will get out of control with very destructive effects. The Mane 6 discovered this, and thus intervened - but not before Equestria and possibly the rest of the world were thrown into very dangerous situations - “which cannot be described”.
Then it means that the pony magic in G4 is too dangerous, by becoming so emotionally unstable that the magical world is torn apart as hostility and enmity spread more and more. This may have shocked Discord who in his long life had probably never realized the latent danger in the pony magic, he now realizes that harmony was not an option but necessary. This may also have shocked non-ponies who have their own magic, and may have convinced them that the ponies pose a serious danger to them. Then it is no wonder that the Mane 6 was forced to take very drastic steps that they will not voluntarily take, to save the ponies and the rest of the world.
But Discord noted that it is not just Twilight, but the entire Mane 6, that is involved in the creation of the Unity Crystals. They were there when Twilight threw the spell that gathered all the magic in the Unity Crystals, and I think it’s because they have moved the focal points all the ponies have, to the Unity Crystals. Until then, the ponies had received magic individually, now they have to do it as a collective through a unified and solitary focus point. But as we have noted in MYM, this was just to fix the problem without solving the problem itself. Which does not make it better, because then it will be easier to lose magic, and if it is returned, the risk of serious setbacks as seen in MYM is too great.
It was this Discord observed, and will thus destroy the Pegasus crystal (which he can not do, and will find out how), so he ran away from the Mane 5 which is kept away with chaos magic. He was willing to give up his magic for the sake of the ponies, and thus chose to grow older in his isolation, but it also looks like he will not comment on the time between S9 and G5. The memories of the experiences from that time, together with his friendship with Fluttershy and his stay with the ponies have made him give up his ambitions for chaos - and this may have contributed to his mental state.
So now Sunny has a big problem that even Twilight can not fix; the latent danger in the pony magic - and her first reaction is to let it be, for she thinks the unity can be maintained. But Discord has a point; as Izzy had learned; magic creates division and thus a basis for dissatisfaction that can break out at any moment. Magic is far too hypersensitive in the face of emotional fluctuations. In pre-Equestrian times, the ponies had a strict casting system in place, and this was probably possible because the pony magic was emotionally neutral, but then came the windigos.
It is now clear that these mysterious creatures had first attacked to create difficulties that caused the ponies to go against each other, (Discord described a similar one in S9, but this can be read in the comic) and then “harvest in” the pony magic that they transform into cold, snow and ice that covers all living things. It was probably the first time the ponies experienced that their own magic was turned against them. And this had created a strong impression, especially after the Hearth’s Warming, where some of the balance was restored. There will be a strong predominance of harmony and social balance in Equestria as a result.
The only solution to stabilizing the pony’s magic that may have been unstable ever since the exodus from the ponies’ homeland is to make it emotionally neutral so that it can no longer behave like a Vulcan from the Star Trek universe. And all Star Trek fans know how strong the emotions are in a Vulcan without his mental discipline. The ponies chose social balance and harmony as a solution.
But as we have seen, it is not enough. And Discord knows that.