The Air Force is jamming GPS. What if an adversary did?

Civilian equipment is often not prepared for dealing with an unexpected war. I don't think this is a problem to be solved.

There's still thousands of planes in the sky whose safety needs to be considered in such a (predictable) event.

It's not a civilian protocol - it's run by Air Force Space Command (the 2nd Space Operations Squadron) primarily for the benefit of the military, but as a matter of policy, the DoD also makes it available for civilian use. The key point is that military use comes first.