The military use the P(Y) code instead of C/A code. It uses two frequencies to help compensating for ionospheric effects, and the spreading function runs at about ten times the speed, so you get much better accuracy.
Since the spreading function is essentially a key-variable generator (ie a cryptologically secure sequence), and has a period which is much much much longer than the gold codes used for the C/A code (iirc tens of years vs about one second!), it's going to be pretty much damned impossible to spoof it, and hence any interference will in effect just be "noise", so will be automatically ignored.
Having said that, they probably do include mechanisms to null out jamming as well, depending on the type of receiver. A handheld receiver can't really do much of that sort of things, but something mounted on a ship or aircraft has more room for complicated antennas, and the power to drive such a system.
Things like PGMs and Cruise Missiles will use combinations of TFR, GPS, laser illumination, inertial guidance etc. You use multiple sources to improve the overall system accuracy, and minimise the effects of any counter measures.