They can create a new ruling for the official scorer — error on the ump. It doesn't change the outcome of the game (wins and losses), but can change the way something is scored. So, tonight's would still be a perfect game, with the batter taking first on EU3 (error on ump at 1B). A missed homerun call would still be ruled a HR, but with the batter stopping at 2B on the error. Official scorer having access to instant replay, but it not affecting the calls made during the course of the game.
They'd never do it, but it could preserve the records without changing the outcome of the game as played out on the field. Then again, I am sure there are plenty of problems with this idea too.