It's not usually some E-4 sitting at a terminal writing the software that runs sophisticated modern weapons systems.
Instead it is a civilian contractor who is writing the code and then selling the software along with the system to the US military, i.e. the software is being distributed for money.
Besides, if you're distributing the application to anyone besides the DoD you're going to have bigger problems than GPL license compliance.
Bob is the Navy. Alice is the contractor.
Alternately, Bob is me and Alice is you.
Either way, the GPL allows it.
In fact, considering all possible outcomes, stopping business is the most desirable one.
The general public, given they are not customers, are not involved.
And those rights are automatically passed on -- if Alice sells the product to Bob and he resells it to Carol and she compiles it and gives the binary away to Doug, Doug can call Alice and demand the source.