So the knights truly believe that the elements can only be used for bad and while trying to protect there country, have no problem attacking innocents and killing good people on the grounds of others having elements. So how do u feel about a possible redemption for them?
Their fate was not shown, possibly because Whitney realized that a too lenient punishment would be too controversial, even for merciful fans. The cunabulans are too Nazi-like, and there is much to suggest that they had caused the collapse of world unity that had existed before Discord’s invasion.
If Danu had not gone berserk and been very close to killing thousands of ponies, it is possible that Twilight would have drawn them to a world conference to judge them or banished them to Cunabula. After that, it means that the heads of state who have become prosecutors, juries and judges - will have no choice but to punish the cunabulan element bearers. Starswirl will have come up with important advice that Twilight must follow, and she had to listen to the others about the prisoners’ fate.
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Take away from the element bearers their magic, since they are of chimerian nature it can mean a permanent death if the element magic can not be separated.
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Petrify them. The harmony magic has this ability, and the Harmony will allow this.
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Send them to Tartarus forever, but then they will only become other people’s problems in later times.
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Send them to Cunabula, but under strong surveillance with a spell that can prevent magical abuse, and then be prepared to destroy the island.
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If Danu had succeeded, he and the other element bearers would have been wanted and hunted to their death and Cunabula would have been wiped off the face of the world. At least a dozen realms and the royal sisters will take care of that. Starswirl would have pushed for execution.
The problem with the cunabulans is that they are a serious danger to themselves and others by abusing their magic, so that they end up being a negative reflection of what they were supposed to represent, patriotism is not meant to promote brutality against different people and indifference between their own people. We do not know why they use harmony magic to “charge up” different magic as with Danu and his earth manipulation magic, or why the elements associated with the temples followed to the opposite as discovered in Ornithia. I think malfunctioning element magic is what had made the cunabulans so dangerous, even to themselves.
In our world, we would have gone for permanent solutions, and then try to seek a compromise with those remaining in Cunabula. The cunabulan element bearers are too dangerous, Danu appeared to have been completely brainwashed. We know nothing about Cunabula, but there is something very wrong with this country.
Whitney has given us an impossibility that in a more ruthless world would have slipped right into, but not in an MLP world. Sombra was killed repeatedly. Chrysalis lost everything she had, before being petrified along with Cozy Glow and Tirek. Storm King was killed. Villains who went too far and are perceived as an erratic danger, ended up being permanently taken out. This was the rule in the MLP G1, and partly respected in the G4.