I would say. Do them carefully and maybe limit your range of motion. See how that feels for a few weeks and maybe things will work themselves out.
This really doesn't make sense to me though. If you are doing heavy ass Military Presses then you shouldn't be having problems with this.
Anyways. If you really can't do them for some reason then dump them and do 3 sets of light shoulder exercsises with dumbells and that should help your shoulders with some flexibility and strenghten them.
I don't know the name if the exercise. But the one where you hold a dumbell around your waist area with your arm at a 90 degree angle, keep your elbow at your side, and move the dumbell outwards, and then back inwards would be good. Or some light laterals I guess.