If WH40K got the Bioware Treatment...

[The Glyphstone]

The problem is this. Space Marines are pretty explicitely engineered for the goal of not feeling moral ambiguity.

Basically, yeah. Space Marines aren't exactly biological computers (except for the GK), but it's hard-coded into them in a fundamental, subconscious level of their being that Chaos Bad, Disobeying Orders Bad, Heresy Bad, Kill The Xenos. When they break these or even consider breaking them, it's a sign that something has gone very wrong and leads to stuff like punitive crusades and purges. 'Better an entire planet die than one demon be be dealt with' is not simply a perfectly rational SM response, but the only one he'll have unless already corrupted.

As an Inquisitor, on the other hand, making such morally ambiguous choices is your bread and butter, and you probably do it on a daily basis anyways. Not only do you have the leeway to make such choices, it's like the Inquisition already has a built-in version of the Paragon/Renegade split that Bioware wants to have babies with, with the Puritan and Radical factions.