One fix would be to expand and emphasize the unfair act rule. Empower officials to, in the event of an intentional foul to gain a tactical advantage, craft a remedy that they think is sufficient to undo the advantage gained.
There is a rule that says if a player jumps off the bench to tackle a player who otherwise has a clear path to a TD, the refs award a touchdown instead of just 5 yards for 12 men on the field. I'm pretty sure that the origin for that rule was a situation where that happened in a Navy game a long time ago, and the refs basically said "there's no rule, but this is nonsense, so we are giving them the touchdown anyways." This would basically be a catch all to let refs address the next "loophole" that's found instead of waiting for it to be exploited and then changing it after it's too late. Obviously, there would be controversy and fans would whine when their team gets penalized that way.
A lot of the recent loopholes seem to come from taking deliberate penalties to get the benefit of time that runs off. Maybe an easier fix for those would just be to, for any penalty, give the unrealized team the option to restore the clock to where it was before the play. Sort of the opposite of the automatic runoff for some offensive penalties late in games.
