I think the development team will try and take timelines into account. The Imagineers weren't originally going to have AT-ATs in the current ride, instead planning a Hoth segment based around Wampas and Tauntauns. Lucas gave them an excuse for Hoth that actually clicks with some EU material that there was an earlier battle at Hoth between the Empire and Rebels and the Alliance returned to Hoth figuring the Empire wouldn't expect them to return.
The Empire banned Podracing, but it's not like the Hutts on Tatooine would give a crap about the law. Could be argued that the droids on Naboo was just some Imperial outsourcing considering all those tax dollars spent on building the Death Star could probably be cutting into money that could have been spent sent sending Troopers and Imperials to the system.
Really, the only current destination that doesn't fit is the random space battle around Coruscant unless there's some "Clone Wars Recreationists Society" that somehow exists during Imperial time.
As long as George's "Screw timelines, this is Disneyland" mindset that lead to all the Disney easter eggs doesn't seep into new movie scenes, we'll be fine.