First of all the Army has flying infantry, they are called Air Assault forces and they utilize helicoptors (Airborne troops are also flying infantry but the planes are flown by Air Force personnel). The only reason the Army is into helicoptors as much as they are is because they are banned from using planes (because the Air Force has that monopoly). When humans start going into space you can expect one of the existing branches will assume that mission and its most likely the Navy...
You were making sense up to that point, but for historical and technical reasons that is COMPLETELY absurd.
To begin with, humans have ALREADY moved into space, and the Navy ceased its involvement in space operations 50 years ago. All U.S. military operations are now conducted through the Air Force, in much the same way air operations used to be conducted through the Army. If a military organization is to spin off in space, it'll branch off from the Air Force Space Command -- which DOES operate in space -- and not from the Navy, which has no spaceflight capabilities to speak of.
Moreover, the analogy to "airborne infantry" is an apt one: the Air Force doesn't need to develop a hundred-thousand-man infantry unit, because the Army has plenty of troops. The Air Force doesn't need to have attack helicopters or gunships or paratroopers; the Army has all of that, they just need a ride sometimes.
Carry that a little bit further: if it was possible to drop paratroopers from modified research aircraft without compromising survivability, would there be any need to build specialized military hardware for that job? If, furthermore, it was possible to arm those same research aircraft with air-to-air missiles, ELINT systems, ECM and ECCM equipment and have those modified research aircraft match or exceed the performance of air superiority fighters from their next closest rivals, would there be any particular need to build dedicated military hardware?
There's all kinds of reasons why you would need a land army, but if you didn't need a dedicated Air Force, why would you bother building one? Same question for Starfleet: if the exploration fleet can outfight anyone else's military, then why do you NEED a space branch of your military?
And was there some evidence that these defense forces were not directly or indirectly under the control of Starfleet???
Unlikely. Backstage material describes them as very large, unmanned missiles designed to shoot down interlopers entering the system. Under normal circumstances they'd be more than adequate; against the Borg, they're just targets.
If they'd been with Starfleet, they would have been, you know, STARSHIPS.