Well she's trying to protect him...I mean,in the genocide run, even when you've showed nobody else mercy, he'll still want to spare Frisk. Yet you can still murder him... And in the event you do spare him, he'll pretty much give away he knew there was a massive chance you wouldn't. To be honest, I don't think he'd be able to bring himself to hurt anyone. If he did, think how horrible he'd feel. He didn't know you'd be killed if you got captured, and he's not even able to bring himself to do that. I can understand why she wouldn't let him join. She cares so much about him she'd rather he felt upset than he died or felt ten times worse.