Nobody is going to stop playing large ships if one out of 30+ crit cards disables a crew function... Stop being an alarmist.
Other possible crit cards could be like something such as : comms failure, pilot cannot gain benefit from friendly pilots abilities and cannot receive free actions. Roll a dice at the end of each turn, if you roll (something) flip card face down.
There is a lot that can be added without disabling the game or getting players from playing in tournaments.
Ignoring other pilot abilities would hit a very specific subset of pilots. Only one of them is even slightly common right now.
Decreased fun.
Increased mandatory cost.
Completely unnecessary, just like the other 500 ideas on 50 threads on the same topic.