Mikan is one of my favourite girls, yes she is a very flawed character, but the simulation shows she could have been fixed and made whole by a supportive environment. Yes, she becomes evil in the real world, but so does the rest of her class, despite being in a much better starting position than her, both mentally and socially.
The fact she kills changes nothing as anyone would with the rememberance disease (which is such a silly plot point) and she got it because she took care of the sick...
If you hate her, you have to hate all her classmates too, otherwise you're just a bully.