How about this; DC Comics has separated all of their lengthy continuities into separate Earths. Every time someone comes up with a new, closed continuity, they just add another Earth with a number (Earth 2 or Earth 76).
Why don't we just start something similar with Star Trek? Right now we would have Trekverse 1 and Trekverse 2, but over time (maybe when Trek has entered it's 3rd re-imagining) it'll catch on.
You know, on thinking it over, I think something like this could be viable. We've already got "Prime Universe" for the original 1964-2005 continuity, and "prime" means "first." So we could have the Prime Universe and the Second Universe. I think that has a certain elegance to it. Or maybe Prime History and Second History, which is also kind of cool. And of course it could be extended to Third, Fourth, etc.
Could we apply this to the comic/novel/gameverses ?
Off the top of my head there's the 80's novel continuity (either including the Rihannsu or giving it another continuity of its own), the Shatnerverse, the relaunch, various runs of comics, ST Online...
Or is it just too messy ?