He did have the ability to get away from his parents, though? He and Val have both run away.
Plus, here’s the thing; even if Franklin did get to Krakoa, through the gate or not, Sue and Reed can’t follow without anyone’s permission. That is literally all Xavier would have to say “Well, he doesn’t want you there so I don’t feel comfortable granting access either,” etc and voila. Legal loop-hole.
In any case, I really can’t see how Xavier could come across as anything but manipulative here. For one thing, he’s hardly keeping Erik from escalating tensions, or even doing anything to alleviate concerns. Rather than say, just offer to take the whole family through the gate for a tour and talk to the parents in any manner that doesn’t feel like a back-handed insult (as in, talking down to them) he just lets things keep building and building into a fight. He’s a smart man and a psychologist at that: he knows better than anyone what it takes to woo parents and prospective mutants; that was tactical alienation right there.