They're offering a service, with contractual limitations that the Pentagon agreed to.

It doesn't seem any different to me than Dominos pizza offering to deliver pizzas to the Pentagon but not to the strait of Hormuz. If that somehow makes the military subordinate to Dominos Pizza, just because Dominos is able to dictate the terms of their own delivery service, then sure, ban anyone in the military supply chain from being able to order pizzas. It would make the same amount of sense.