Aliasalpha: You talk to your fellow marines about how best to purge the alien, the mutant and the heretic
Well, see, that's just what I'm getting at. The forces of the Imperium fight amongst themselves almost ass much as they fight the enemy. There have been numerous occasions in codex and in for-the-hell-of-it gameplay of Marines fighting Marines, Marines fighting the Guard, Guard fighting other Guard, the Guard fighting the Inquisition, the Marines fighting the Inquisition, and the Sisters of Battle indiscriminately burning everything. And the Imperium is supposed to represent ORDER.
In other MMOs, people of different races can still play together (Alliance or Horde?), and there's usually some in-story justification for why this is so. Warhammer 40K's setting is based on extreme xenophobia, so I imagine that mixed groups of players aren't happening.
That said, from what I see, it looks like there's only a few factions to choose from. I suppose there's no interparty conflict if you've only got the choice to play Marines, Orks, or Chaos.