User blog comment:Druidinhiding/Alternate Ending Theories and Thoughts/@comment-4650675-20121227214802/@comment-5674726-20121227220737

After all, if Arthur brought magic back, Morgana would have no reasons to still fight him, and would have found no supporters whatsoever!

Well, she might still have had the Saxons on her side, but I don't see her fighting if Arthur restored magic to the kingdom.

I don't doubt that Morgana believed that Arthur would be better than Uther in the sense that those who were falsely accused of magic or who had the misfortune to be tricked into helping a sorcerer would be better off if he was the King. However, she had good cause not to believe that people like her, who were actually "guilty" of having magic, would fare any better under Arthur's reign than under Uther's. Unlike Merlin, she didn't have a prophecy about Arthur restoring magic to Albion. For her, there was no light at the end of the tunnel.

At no point during his reign did Arthur legalise magic. When Arthur said that she couldn't blame him for Uther's sins, Morgana specifically told him that it was too late for that, since he had made it clear how he felt about her and those like her. He had the power to change the laws against magic but had chosen not to do so. That would suggest to me that, even if a reconciliation wasn't on the cards, a cessation of hostilities on Morgana's part would have been a strong possibility, had she been given reason to trust that, under Arthur's rule, those with magic would be accepted.

If Arthur was just going to follow in Uther's footsteps re. outlawing magic, then from Morgana's perspective, the only solution would be for her to remove him from power and make the necessary changes herself.