If WH40K got the Bioware Treatment...

[Wraith]

How about 30K then, with the protagonist being Horus?

This would probably be the only way that you could have a conflicted Space Marine in the lead role, I think - one who serves in one of the (soon-to-be) Traitor Legions, but isn't one of the truly damned ones like the World Eaters or the Night Lords.
Those guys were genuinely and universally damaged beyond repair in short order and as such didn't get much of a choice in the matter, but let's take someone else - Sons of Horus, or Death Guard - who is torn between following the order of his Primarch, whose loyalty is slowly disintegrating before his eyes, and the edict of his creator the Emperor of Man.

There's your sliding scale of morality between 'Loyalty' to the Emperor/Imperium and 'Betrayal' by following the increasingly-corrupt influence of your Primarch. From your perspective, obeying both is the 'right' choice, but it would come down to how far you're willing to go before you're forced to draw a line in the sand.... if you can at all?

And there's your multiple endings: do you Fall and become one of the Veterans of the Long War, or do you defy your Primarch in His name and become one of the few Loyal remnants of your Legion?
And everything in between; do you Fall quite a way, but some of your noble actions mark you apart from your truly degenerate brothers and you are cast out to walk the stars alone? Do you struggle to remain Loyal, but a few slips here and there sees you rejected or even killed by the Imperium? Or do you try to walk the precarious line between the two, and die in shame for failing in your duties to both sides? And numerous steps in between.

In the same vein, I don't think a fully fledged Inquisitor would fit the role because most of the time they are beyond reproach - there's more scope for moral conflict, but still not a lot as generally Inquisitors have a very unusual system of morality.
They are probably the only 'good' organisation that can reasonably commit genocide upon multiple worlds via Exterminatus, for example. In 40k canon, consigning a billion souls to death to prevent the outbreak of a single daemonic incursion is preferable, provided that it can also be justified to the satisfaction your peers as Cheesegear has explained.
As a PLAYER having to make the choice - Genocide = Good - this might be a little too abstract to explore easily.

As has already been mentioned, playing the role of an Interrogator in an Inquisitor's warband would be easier to portray. That way any moral quandries can be interpreted as your character growing into his role as a fledgling Inquisitor - those who shy away from the hard choices and try to compromise get the 'bad' endings for failing to commit to the Inquisition's cause, and those who embrace such choices are the ones who accomplish their goal; to become elevated to the full rank of Inquisitor.

And, of course, as an Interrogator a lot of responsibility and delegation is placed upon you as your are the Inquisitor's Second-In-Command, so with that sort of autonomy you still have the chance to encounter Xenos and either kill the outright or advise your Master to allow you to use them as assets, and to encounter Daemon artifacts that you might be inclined to use for your own benefit, even if in secrecy. The Ravenor books use this particular theme as a major plot point, so it's perfectly plausible to ALSO have a sliding scale of 'Puritan vs. Radicalism' side-by-side with your 'Loyalty'/'Conviction' scales.

This way, the Player can be taught the game's morality system by the Inquisitor NPC and then be left to decide how much of it they want to participate in in order to try and become an Inquisitor, as well as working towards what sort of Inquisitor you want to be in the process.
Simply starting out as an Inquisitor will either require you to already have this foreknowledge of the setting in order to get the better endings, or to have a lot of tedious conversations where a supposedly graduated Inquisitor has to be told over and over what his job is and how to do it, in the same way that an Engineer-class Commander Shepherd has to keep asking stupid question about how engines work, for the benefit of the Player.....