As with any workplace/job that enforced this bs in the first place, I wouldn't go back without a complete overhaul of the management. I would want to know 100% that this kind of environment would not happen again and that nothing would be held over my head for standing up for myself.

Also, I'd negotiate a raise and better benefits (although this is the military, so I know that'd be a tough one). The unvaxxed are basically going to be the European peasants dealing with their liege lords after the plague blasted through.