I'm sure the Science Channel paid much less for the rights to air it than they would have had to pay to develop it, so they could get minimal ratings and still do okay. That doesn't really help out with new show development.How did Firefly do on the Science Channel?
It would be great if they could follow the History Channel's lead and start funding scripted show development, but my instinct is that History has a broader reach and more money for new series development. (On Comcast here in SF, History is on the basic-plus tier and Science is one tier up, which limits their reach and their share of cable subscription revenues.)
As for the military angle - Star Trek has established its philosophy of being "kind of military but not really." That's their unique identity, so trying to shoehorn Star Trek into some current real-world military tradition is missing the point. This is a future speculative military of a type that's never existed and probably never will, just as it's doubtful humanity will ever "evolve" beyond religious or even national identities, and I also have my doubts about the death of capitalism, ever.
Star Trek presents us with these unlikely scenarios and then asks us to suspend disbelief and just go with it, because that's what sci fi does.