Interesting. I'm not sure if I agree. Not meaning to deny your viewpoint at all, but, to my experience, anxiety doesn't go away just because you're aware that there's nothing to worry about. To me, her concern is more a result of being, well, traumatized. Her son was raped. She's having trouble letting go because, last time she wasn't there to protect him, he was violated. That's enough to give someone a complex. I don't think she'd be having an easier time with that, regardless of what she knows.
As for James being targeted for being Peter's son... If that were the case, yeah. She'd be pissed.