The best way to deal with it I've found is first, make sure follow auto pilot ships is not checked in the options. It's under interface. Then zoom in to a dead part of space while the auto pilot ships are moving. When they're offscreen and not selected they move almost instantaniously.
this is also what i do, and multi-task as well. the great thing about TBS games is that you can walk away from them and you won't really miss anything important.