The withdrawl penalty is a good thing. I've read the entire thread, now, and every circumstance put forward as to why it is bad - EVERY CIRCUMSTANCE - is a situation where earning the penalty is pretty darned easy to avoid.
Party keeps withdrawing? Use Ready Check before signing up for the duty. If you're signing up for something as a partial party, chances are good that they are all people that you know and trust. The Ready Check gives them a chance to let you know that they haven't gone afk. If you're signing up as a complete party, you don't need to worry:
So, trolls have no foothold at all. They can't join Party Finder, and nuke some poor, unsuspecting party with multiple withdrawls to inflict penalty on them, because a party finder party will be a full party before it enters, if the organizers have a lick of sense. To be trolled, you need to have the hilariously bad sense to enter duty finder with a partial party composed of strangers - and, after doing so, try again twice after they troll you the first time. It's safe to say that these are pretty fringe situations we're talking about, here.
As for incurring a penalty for unavoidable issues (in bathroom when commence appears, in the middle of a long and risky craft, engaged with an enemy and can't escape and change in time, etc), that is why we have three strikes. If you fail twice, take a little care before signing up a third time. If you're on your last strike, DON'T start that risky craft, DON'T enter a FATE that you won't be able to leave in time, use the bathroom FIRST before signing up, and so on.
Is this the best solution SE could have come up with? Perhaps, perhaps not. They certainly should have started by removing all in-progress indicators from the commence window (it was idiotic to include those in the first place), but this solution isn't bad by any means.