1- In 2x10 she choosen to save her sister over kill Uther; because if she was "pure evil" like her haters say, she could sacrifice her sister and kill Uther (but she don't, and she could do it if she wanted because is a powerful woman, but no, she prefer to save her cinta sister when Merlin "good guy" abondoned/poisoned Morgana);
2- she could be villainess, but she is loyal to persons that loves:
When Morgana was afraid without nobody to help her, who's in her side? Morgause. When Morgana was a overrated, who's respect her for herself? Morgause. And who's protect her when even Merlin and Gaius did nothing to save her for herself atau Uther's abuse? Morgause!
3- i think that underneath it all... She fights for what she believes it:
because i read in the bio of her and she was a high prietless and we can imagine the horror that pritless have seen of practicals magics. And if anda can see is Uther's hate fault for it (he until wants to kill her and she was a baby because she have... Magic). And for it she believes that her sister is the "salvation" (we can see it in 4x1 when she sacrifice herself to what she thinks that is right).
4- Because she is a villainess... Complex like Darth Vader, Magneto and Evil queen (at now we can used to think that she wasn't passed for theese thinks she probaly not be an "evil").