What's wrong with "do overs". We do that after inadvertent whistles - another crew screwup.
With IW's there are provisions to alleviate the damage done, if the team in possession so wants. If we start going back in the down sequence, how can you make sure that the decision is even close to equitable?
Assume that there was a fumble on the first down play. Would you still go back and do the down over after fixing the penalty enforcement? Or, assume that we run three plays, minor gain for team A, and THEN the L comes in. Would you still go back?
This is a freak occurrence, I really don't see any need to fix this by a rule change to allow going back. Take all the time you need before making the ball ready, yes, and get it right even if it takes you half an hour.