I read it as the later, too, but found out that most reviewers took at as the former!

Really? The mind, she boggles... but I guess it's perceptions like this that we owe Hiro's "You care too much." speech to.

But whatever his power was, being Peter, he'd be likely to want to talk with Nathan about it, and she kept all the superpowers information from Nathan until the proverbial last hour.

I wonder why, actually, for purely logistic reasons. If you really want your kid to be the future leader of the world, and to be mutant-friendly, wouldn't you raise him in the awareness of being a mutant? Otherwise you would be in danger of having a Roy Cohn on your hands, which seems to be exactly what happened!