If WH40K got the Bioware Treatment...

[Cheesegear]

First off, let's lose the 2 point morality system, as despite 40k's strong focus on the Chaos/Purity scale, that's not all there is, and some things don't really make sense with regards to it.

It's not a two-point morality system. It's a sliding scale. You either have Corruption or you don't. 'Purity' is not something you have, more like, Corruption is something you don't have. Second, Inquisitors and their followers definitely do have it. If you don't calling it 'Morality', call it 'Reputation' like from Baldur's Gate. Or Karma from Fallout. Those work fine. I have no issues with that.

I dislike Mass Effect's system where you can have Renegade and Paragon at the same time. Which didn't make any sense.

Second, being 'Pure' makes the game more difficult. But you get to live. The bonuses you get for Corrupt decisions make the game easier. That's kind of the point. But, being Corrupt means you generally die at the end.

ME's Renegade and Paragon have no meaningful difference except for dialogue options.

Then you have another scale, which needs descriptors, but involves choices that aren't dealing with Laws and Social Mores. This is where stuff like temporary Xenos alliances would fall.

What? Allying with Xenos is definitely against the Law, and most certainly is a social moor. Have some corruption Lose some reputation. Whatever you want to call it, the system still needs to be there.

'Corruption' is a catch-all term. That definitely applies to Lawful situations. It's like saying that issuing Exterminatus doesn't involve dealing with Daemons, therefore I can do it as much as I want. Or killing civilians is legit. Think of Corruption The Scale, as how much other Inquisitors and Lawful Institutions hate you.
Remember, in my version, you're not actually an Inquisitor. You don't have the badge. You're just some schmuck on the street.