Yeah, the decision to roll back on damage decks was pants-on-head stupid, but FFG has a history of going for the hard-on-player decision first (the Scum dial fiasco) and changing it to be the most accommodating to everyone.
I still think the ideal way to handle it would be to have players assign damage decks to their opponent, to represent their ships choosing a target priority ("Target their secondary weapons!"). It'd be more thematic than simply choosing the deck that is least painful to them. However, I also appreciate the counter-argument from people who don't want to have to share their decks with opponents who may not have the best hygiene.
I think mostly you'd get an argument from opponents who only own the one deck.