I mean i don't hate monika or anything in fact i love the conversation in act 3 since it was down to earth and very supportive. But when you delete her, she realizes that what you wanted to be happy was for the world of DDLC to have a happy ending with everyone else, so she rewrites the story to do just that. If you listen to her in Act 3, she tries to give you a lot of advice to try and help you to be a better person. All Monika ever wanted was to make that real person happy.
Actually, she wasn't trying to kill them, but to just make them unlikeable, but anyway, she did it because she wanted to be with you, someone real.
But Monika wasn't killing them 'because' they're not real. Except when we kill people in video games, its usually out of self-defense, not because they're not real.
