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.
If we all go with my idea and stick to it, it'll catch on!