It's a healthy discussion to have, really. The way the wiki is currently structured in regards to non canon information is prone to misunderstandings, so trying to figure out what could be done differently is not a bad thing.
One thing I can think of right off at least, that would help it some, would be to nest any theories and information that apply to a specific campaign as a subsection of that campaign. So information on the Starborn, for instance, as well as any fan speculation on them, would only be accessible through the Starborn campaign page, Speculation on the origin of the Nyarlathotep (btw, if I spelled that right from memory, I deserve a cookie) only from the Derelict campaign page, and so on.
It would clean it up some, if nothing else, and keep things in proper context as frankly these things can really only be understood within their respective campaign settings anyway.