Yes, that last one was a little bit of a catch 22. With no cards you cannot take the players word on what he had. Nor can you reliably fish it out of the muck pile. Nor can you put a player with no cards up against another player's hand.
Honestly, however, I think that they made 1/2 of the correct decision; he should have received a penalty of a one round sitout to go with the 60k he had to pay.
As we did not see the part where he mucked he might have actually done it on purpose (might have). I mean, they allowed him to save his MTT life, but it is clearly the players responsibility to pay attention at the table, so it adversely affected her as well. I understand mistakes can happen and it's a brutal pace with lots of pressure, still - it's up to you to know where your at and what is going on regardless of stress.