There is no point transporting 5 Space Marines across the galaxy... if you are just going to throw them into pitched battles at a whim. This is why Space Marines are hoofed around 100 or 300 at a time minimum. But the inquisition isn't here to fight pitched battles. It's here to flush out the unseen enemy, enemies that might be equally capable of dispatching squads of normal troops as a Space Marine but more difficult to find.
I seriously doubt that it's common practice to take a planet with 1 company of Marines, I don't remember a situation where that's the case and if pressed to or if they encountered a backward world like ours (which incidentally has 194 individual armies arrayed against each other, not a situation that is likely in the future) I'm sure they wouldn't imediately send there forces to every corner of the world to kill every soldier on the planet when they could pounding the planet into oblivion with the future arsenal of several mile long space craft while the Space Marines persue actual military objectives.
Regardless though, this isn't about fluff or realism or (lack there of) it's about gameplay. Games where you have no chance of failure are not fun for long, games which don't have any better gear than the stuff you start with take a huge part away from the players, and games where you spend all night in one small combat are taking away from much better oportunities.
