TSA is unbelievable sometimes. I understand they have a job to do but dayum! When I deployed to the middle east for the first gulf war, we flew over on a military C-5 Galaxy and flew back on a civilian 747. Back then (pre 911) there was no problem with customs either way.
Most, if not all, civilian airlines can be pressed into service by the military if need be. But the ops tempo now is insane and the military airlifters are hard pressed to meet their commitments. It may simply be that there were no military aircraft available during the required time frame. It's hard to say.
Whatever the case, your frustration level is gonna be pretty high when you encounter situations like that.