Actually we (the military) could decide to just turn 'em off. There was some talk about those kinds of plans right after 9/11, and that capability exists over war zones. You can program in a code that makes them unreliable unless you have the applicable code key in your own aircraft. There's also the whole jamming thing.
I think the "free flight" thing is only going to happen anytime soon in higher altitude airspace, probably Class A and above at the highest. Kind of the way RVSM did. There are too many old airplanes operating below 18000. Another thing that kind of hampers it is that the military is way behind the civilian world on GPS, datalink, etc., etc. and they aren't moving forward with any kind of speed, so they will resist the FAA HARD on making these systems a requirement.
Also, it seems like all of ICAO can't seem to get its act together regarding exactly what systems are required in what airspace (in terms of RNP versus RNAV versus BRNAV/PRNAV, RNP .1, RNP .3, RNP 1, etc., etc.) For example, an RNP 1 airplane meets the same navigation performance as an RNAV 1 airplane, but they're two separate certifications. Or if your airplane can meet RNP 1 than logically you would think it could meet RNP 2 and above also, but those are ALSO separate certifications. That is going to slow things down also, as nations dicker back and forth over exactly what navigation standard is going to be required, where.