Because then they might find a way around it... better to let them think it's working, then when they try to fly it then they die and it autoplots a jump to the nearest Shivan base. So they get their fighter back. Sort of like, did you see Stargate SG-1? They put a failsafe in the Goa'uld fighter that made it fly back to the base when it was captured.
See in FS1/FS2 a Shivan fighter always gets captured, figured they would get wise to that and take precautions against it.
If I can find a way around shutting down everything, I can find a way around shutting down of one system. Most likely. Just sayin'.
Better off not letting them fly anything at all than just nerfing one capability. Just make it shut itself down and fly back with the live pilot inside, for questioning, or disposal. Don't wait on them *discovering* how to activate something which will kill them. That's really silly. What if they never activate it and use it to infiltrate your ranks again anyway?
Disabling one non-critical system solves nothing. Shut the whole thing down, have it seal itself, and return to the carrier. Might still bite you in the ass due to giving your position away, but at least you're eliminating the possibility of it coming back to haunt you as much as possible.
Don't bank on "OH HEY THIS IS A WORKING FIGHTER I WONDER WHAT THIS BUTTON DOES>", why bother with such a stupid failsafe? It's not very "fail safe" at all, and is rather prone to actually failing to do anything.