User blog comment:Sir Dagonet the jester/The strange case of Morgana Pendragon/@comment-5674726-20150318192207

I think that there is a very simple reason why Morgana was turned into a villain: The writers weren't prepared to allow her to be anything else.

Had Morgana remained an ally of Arthur's, it is a safe bet that she would have been the person most likely to convince him to change his view of magic. They grew up together so, not only would Arthur be able to accept that she could be a good person and have magic, he would believe her when she said that it was something she was born with rather than something she sought out. No way were the writers going to let somebody other than Merlin be the one to help Arthur see the light.

On top of that, it is probable that a good Morgana would have tried to work within the system, at least to a limited extent, to help other magic users. I could see her becoming a sort of double agent, like Lady Marian in the BBC Robin Hood, trying to balance helping magic users who did not pose a threat with not endangering Camelot. It could have been a good and plausible storyline for her but her action would have served to emphasise Merlin's inaction, and I can't imagine that the writers wanted that.

Basically, a good Morgana would potentially upstage Merlin.