Actually Ender's Game, particularly the short story, was pretty well written. Of course, it was written to drag you into the author's viewpoint about how to think, which is a pretty weird viewpoint, but I'd criticize the viewpoint before I'd criticize the writing. The story had quite an affect on my thinking when I was in my twenties.
As far as the biblical verse goes, it seems irrelevant. The reason for laws on molestation and statutory rape is that we've decided as a society that people below a certain age aren't realistically able to give consent. In order to protect their rights, we make it illegal to have sex with them. This is a case of conflicting rights: the child molester wants to fuck the child, and the child has a right not to be fucked. So while it's hard to see how anybody could disagree about the interpretation of the bible verse you've paraphrased, if you paraphrased it accurately, it has no bearing on whether we should be tolerant of NAMBLA.
In fact, I think we should be tolerant of people who want to fuck children, but not to the extent of letting them do so. Having desires that can only be satisfied by taking away the rights of others is not a happy state of mind. A compassionate person would try to help the person who has that state of mind. At the same time, they would try to prevent that person from acting on that state of mind. Preferably in a pleasant custodial setting.
You could make the same argument for gay people, but the issue of consent isn't present if both are old enough to give consent. If you feel that their state of mind is still wrong, you are free to tell them so, and to try to help them. And they are free to tell you to fuck off, and to get a restraining order if you don't.
And by the way, if someone is openly a member of NAMBLA, chances are they're going to have trouble getting hired to clean toilets, much less be CEO of Mozilla.