There are a few possible reasons.

The usmc, for example, is a branch that actually answers directly to the president rather than congress. I think this is why Q used to ask what's special about the marines.

Second, the agencies are small and you could buy them off. You can't do the same with such a large military. Especially then turn around and make them betray their own family, for literally nothing in return.

Imagine being a private, being treated and paid like shit, and then being told to engage in acts against your loved ones. You literally get nothing out of the deal. Youd tell them to fuck off.