I really liked the idea of the MACOs, who could be assigned to a starship whenever military force was necessary.
Actually, the whole point with their introduction seemed to be that they never
did that sort of thing, which is why Forrest thought that Archer might be offended. After all, Archer had heavily armed troops of his own, in Starfleet uniforms, to do whatever internal defending his starship needed. And that was with an explicitly unique exploration-oriented starship, suggesting that most other Starfleet vessels would be dedicated to combat. (Or then to asteroid trawling or buoy maintenance, but somehow I doubt that.)
The Military Assault Command vs. Starfleet Command thing sounds like classic interservices rivalry: the MACO forces do their own thing, possibly with their own ships, and when a MACO contingent is sent aboard a SFC vessel to do the job of Starfleet's own "Marines", it's naturally considered an insult.
Whether any of that carried over when the UFP was formed, we don't know. We get occasional references to Commands other than Starfleet Command in TNG and DS9, but all of those seem to be subservient to Starfleet Command, rather than equals and rivals. Then again, all of those Terraform Commands and whatnot pop out of the left field and then disappear; statistically, something like Military Command (in the old sense of military = ground forces) might exist but remain unseen, in TNG at least. In the war-heavy DS9, that's rather unlikely, though.