I think you really can, just keep police it like you always do, the only difference is that this time it will be less simple than "ok, you paused you lose", because you will have to take the timer and the meter into consideration. I mean if you can set a concrete rule then people will follow it even if it is more complex than the current one. Now about the 50% of meter I talked about, it is just an example, it isn't a definitive idea; but, why do I think a new rule is important? Well, if you watch the pl fk match closely you will notice that pl was about to take the first round for him, so I honestly think he hadn't push the button on purpose, it just would have a negative impact on him (as it happened, because the current rule), so it is more than obvious that there is something wrong with the "pause=lose" rule, I know it should be some kind of penalty to the person than paused but losing the entire match is too much imo.
I really doubt a person will pause on purpose if he has the lead, but I can imagine scenarios where it could benefit him; nevertheless, the new rule should punish that, I know you can't know when the pause was on purpose or not, that is why I said if you don't have the lead then the current rule should be enforced but if you have the lead then a modificated rule should be applied. someone mention why not just removed the pause button from the controller?, but I think you need that button for other things than just pause the screen, plus few people will actually want to own a controller just for tournaments, I guess they use the same controller they use when playing at home.
Again, it is a matter of discussion, someone said that in other games like sfIV you lose a round and not the match; IGAU doesn't have rounds, the current rule doesn't take that in consideration that is why a new rule should be placed to deal with this kind of differences, but bringing the "no, pause=lose, /thread" attitude doesn't help, what it is needed is more discussion.