The Space Shuttle was designed to do several things that had nothing to do with NASA's purview: To launch anti-USSR spy satellites into polar orbit from Vandenberg, to reboost and repair those satellites, and to steal/recover USSR-owned spy satellites, taking them into the cargo bay and landing at a US runway in order to recover their technology in the event that the USSR got ahead of us again. This also applies to US-owned satellites at risk of reentering over the USSR to prevent their tech from catching up.
In order to do this, they made the whole thing incredibly expensive, and sacrificed a lot of capabilities NASA would have rather had.
That's what this is for. It serves as a functional military Shuttle analog against small payloads, and as a beta for a manned X-37C or X-37D against larger payloads.
I haven't time at the moment to check, but I'd assume GPS and GLONASS birds are in geostationary orbit (or whatever they call that now), which would complicate matters significantly. I imagine the Air Force probably has some sort of weapon in mind for such cases, but I wouldn't begin to know how to guess what that is, except presumably a big rocket, whose payload is a small rocket, whose payload in turn is a tiny warhead with some very precise attitude jets.
NASA never wanted a "space truck". Ever see 2001: A Space Odyssey? NASA wanted something along the lines of the spaceplane/station/moonbase system depicted in the first act; the Space Shuttle program was all they could sell to Congress, largely thanks to the efforts of now-deceased then-Senator William Proxmire. (If you've ever heard a science-fiction fan curse that name and wondered why, now you know; if you want the full story, read the book whose URL I just edited into my prior comment.)
And, yes, "its [sic] easy to point the conspiracy theory finger when the military is involved." It's easy to do a lot of things, which is not the same as saying those things are sensible or worth doing; ignorance, especially of the trivially addressable sort, is no excuse for foolishness.