Here's another suggestion, albeit slightly ridiculous: have seperate threads for anime-only viewers and anime/manga viewers. That way, both sides can freely discuss and/or freely speculate what's going on during the series.

On a more serious note: for any other anime series besides Naruto, why not just have people start spoiler threads if they wish to discuss "what's already known." Like how movies or tv shows are noted in our general discussion section, we can have "Spoiler: (insert non-spoiling title of topic discussion here)." That way, we don't have to reorganize the entire site or add spoiler tags and people would automatically know that they are entering that particular thread at their own risk.