Not sure you want the stealthy $80 million dollar plane packed full of restricted electronics and bombs to land at an insecure airport full of civilians.
Also: in air refueling and carriers mean the plane may not be anywhere near a safe airport.
Mostly these jets fly above NATO countries where nobody is going to fuck with it. I guess such a system would get turned off when flying somewhere unfriendly.
Generally, yes. Better to destroy dozens of aircraft than let an adversary discover a vulnerability that compromises all of them. Of course the ideal would be to not have a problem in the first place, but by the point you're considering having a pilot eject that's out the window.
Also: in air refueling and carriers mean the plane may not be anywhere near a safe airport.