Has the EU ever done time travel or alternate realities? Not "what ifs", but actual Trek "mirror, mirror" type alternates.
I heard there were some stories called "Star Wars Infinities" where the original trilogy stories were altered - like, what if Luke died on Hoth and Han tried to take the Jedi training, or what if Vader survived the duel on the second Death Star and went back to the good guys (imagine Vader in stark white armor instead of black). They're not in "continuity", though, just "what if" stories.
I don't foresee the new movies being weighed down by books and comic backstories, though, and since SW is more space opera fantasy than Star Trek, I don't think there are any avenues for allowing the alternative universe type of out that ST 2009 took.