The developers (whomever they may be) wouldn't respect the lore letter-by-letter in a WH40K game, simply because it wouldn't be practical to do so for a WH40K video game, be it MMO or anything else. It would otherwise need to be specified that the game in question is a "real take" on the actual lore rather than something more... say... adventurous and daring (therefor not exactly respecting all aspects of the lore). The original Dawn of War is a good balance demonstration of pure game-play related adjustments VS fluff elements/inspiration and "rules" so that it can ultimately be enjoyed as a video game per se. If you want lore with entertainment you can play tabletop WH40K. Although I do agree that DoW2 on its own even though is a video game does portray at the very least the Space Marines in a more "lore-friendly" manner than the original DoW did with its massive armies (of Space Marines that is) on the field at once (whereas in DoW2 it is more focused on specific squads with named infantry, as it "should" have been if you want to point at the lore as a reference material prior to developing the game).
Additionally, a lot (if not most) of the gamers whom happen to simply "like" the WH40K franchise due to either Dawn of War or DOW2 (or any other DoW games) haven't touched tabletop WH40K in their life and probably never read a single WH40K novel or codex. That in itself isn't a "bad thing" at all, but the developers wouldn't necessarily make a WH40K game "just for the franchise fans" whom happen to know the actual lore in details. That probably wouldn't be financially viable enough, so they'd have to go fishing where the fish bites. The targeted audience of pretty much any WH40K game wouldn't mind or at least wouldn't be aware of the "real lore" of the WH40K universe (at least not in details), and therefor wouldn't exactly "complain" that 'x' or 'y' scenario presented in any WH40K game makes "sense" (or not) such as playing as Space Marines and devastating hills after hills of fixed fodder cultist mooks to level up from in a MMORPG style game.
They could easily make an MMORPG out of the WH40K franchise though, you can make an MMORPG out of pretty much anything anyway. That doesn't mean it'll be successful, I'm just saying you can make an MMORPG out of anything really. But if they do they'll have to "adjust" (balance) both lore and/or game-play mechanics so that it can be enjoyed by everyone, especially if they are paying a monthly fee (heck even if it was F2P). I for one love the video games "take" on the WH40K universe. I do prefer the way it is portrayed and detailed from the novels and the codex entries, and I did play my share of tabletop WH40K a couple of years ago (haven't since at least a good six years or so by now though). But ultimately I also like the games (especially DoW1), although I perceive them as an alternate "vision" of the universe since I understand that for the current WH40K games that we do have none of them could actually follow each and every single cemented rules (and events as depicted in novels or codex) of the real WH40K fluff to be what they are.
I think I would actually really like a WH40K MMORPG (or MMO FPS), probably action-based with dynamic combat in the veins of TERA (can't really look back at the single-target selection system anymore since I played TERA's dynamic combat system, I think I'm spoiled now). I wouldn't mind much about the lore in such a game and that's the entire point I guess. If I want WH40K lore I won't look for that in a WH40K game as a general rule, especially not in one that is an MMORPG. If the devs feel like it they could have players of such an MMORPG be able to create a male or female characters of any factions you can think of and they'd probably all end up in the same hub worlds or cities together which wouldn't make any sense whatsoever, but in the game itself it could still be enjoyable for "what it is", rather than "what it 'should' be". Can you imagine Dark Eldars players buying goods from NPC Chaos Space Marines vendors in an Imperium of Man Hive World (hub) whilst a mob of Craftworld Eldar, Kroot, Space Marines, IG grunts and Orcs go about their daily business in the surroundings, without a single fight? Well not "in the lore", sure, but in a video game that wants to be an MMORPG "based on" the WH40K universe? Heck why not.