Yeah, you're kind of in a bind. When they release the EE, people will still have the original D:OS that they can use to play your mod, though I doubt many people will want to go back to the worse version of the game. You should probably just release it now, even though there's probably not too many people playing D:OS right now.
D:OS 2 is only being kickstarted right now,so it won't be out until at least late 2016.