Not saying manipulating people is good, but I'm pretty cautious about labelling people evil, and we still don't know what Ella's endgame is. So long as it's a good outcome, I don't think you can unequivocally call her evil. I generally reserve that for people who have negative goals, like genocide, or neutral goals that they reach through negative means, like serial killing (the goal is pleasure).
There's no reason to think Jake would have fucked up Daryl's brain the way he did Mia. That only happened because of the stress of Mia finding out his secret and deciding to tell the MC.
She didn't use Mia as a hostage, she used her as a bargaining chip. Ella will fix Jake's mistake if Jake does what she wants. She isn't threatening to harm Mia, just to not help her, and she's under no obligation to help Mia.
The MC isn't dumb, he just doesn't think, which ultimately stems from his apathy. It's not that he can't put the pieces together, he just doesn't feel like it.