Maybe create separate sub sites for each one?
Good heavens, no! The Catholics and the Baptists and even the Mormons get along fine at Christianity.SE, and the Sunnis and the Shias coexist peacefully on Islam.SE (well, sort of), and heck, if we want to talk about real religious conflict, Haskellers and PHP users even manage to tolerate each other on Stack Overflow!
It is eminently possible to have a site that represents the views of multiple different schools of thought. We just need to follow a few simple rules.
- If you have a question about a specific school, mention it in your question, and use the appropriate tag, e.g. theravada or mahayana.
- If you post an answer based on the doctrine or viewpoint of a specific school, mention it in your answer, citing relevant sources if possible.
- Be nice. This means (among other things) not getting into argumentative wars. Don't let sectarianism ruin this site.
That's all it takes!
Also, from a practical point of view, getting separate sites for different schools of Buddhism is simply not going to happen. If Stack Exchange was open to that possibility, I'm sure they would've split Islam.SE long ago, because internecine conflict is a serious problem over there. The idea of splitting Islam.SE has been discussed on their meta; it was generally agreed that that would not be a good idea.