As many have said, some debates may never be settled in Trekdom - Trek being an utopia as well as a Sci Fi series, coupled with the lack of coherence between the different series and even inside a series makes it quite easy to have as many interpretation of a given aspect of the world as there are fans. Not only do we have the Dreamers and the Militarists byteknight described (and very well by the way), but many other factions or subfactions - the money vs no money, family onboard vs StarFleet only, all greed eliminated vs it's easy to be a saint in Paradise, TOS vs TNG, etc, etc, etc. Therefore, I think any view about the Trekverse will meet roughly one supporter for 5 or 6 detractors.
But I think there's another fact as far as games are concerned, and it's quite simply the type of games that exist. I doubt Activision said to Paramount : "Right, we consider StarFleet to be militaristic, so we'd like it to create a game centered on an elite force team that is sent on dangerous missions", but instead "Hey, we'd like to do a first person shooter in the Trek universe, and we have this concept". Same for any "militaristic" games like Armada or Bridge Commander.
So what Paramount has to choose from is either be very strict about which games they admit, and thus don't have many Star Trek video games being produced (while in the mean time you see every part of other franchises universes being turned into games), or accept that the most successful types of games are turned in a Trek flavor, even if it means to diverge a bit from the serie's ideal or canon (like being able to create a few dozens of Sovereing class to stop the squadron of Borg Cubes in Armada). I don't think that, from a marketing point of view, there's much room for hesitation here....