The first Inquisition was made to commit genocide on the Cathars, the fact that the word itself means something else is irrelevant. If Ted Bundy had called his killing of people Operation Blue Skies and Puppies that wouldn't have made it any better. The Inquisition was a vile institution and Bioware are glorifying it by making it seem cool and something good.
The swastika doesn't mean anything sinister either originally, paint one though and you'll be seen as it.
We'd be very limited in our choice of media with this logic. We shouldn't even have this game, Inquisition or not, because it glorifies the vile act of war. We also definitely shouldn't have the Mass Effect series, as it glorifies...hmmmmm, there are a few decent targets: war again, happiness in slavery for the drell, xenophobia and intolerance if you take all of the renegade options, gun violence and violence in general, thievery through Kasumi, etc. No Jade Empire either, as its partially based on Wuxia China (and mostly Bridge of Birds, fabulous book), and China has some very repressive periods (side note: Not picking on China specifically, I'd bet it's pretty hard to find a country that didn't horrendously abuse some group in their history). Black Whirlwind is probably enough to get the game censored by himself, never mind all of the other cruel things you can do. Better remove the KOTOR games too, as once again we have the glorification of violence and war, especially in the Mandalorians.
And that's just me extrapolating reasons from what your post seems to suggest about your own values. If we open it up to a variety of different value systems, we get even more reasons for censoring this game, as well as every genre. Now, there's no reason we can't have a reasonable discussion about what is and isn't appropriate for media to cover in certain ways. I personally think that no topic should be censored in media -- while I'd prefer that sensitive topics are treated with class and respect, I understand that these are very subjective notions, and what I find respectful someone else might find deeply offensive. With that thought in mind, I'd rather we err on the side of allowing various interpretations of topic -- if something is truly unpalatable, well that product will simply not sell, potentially taking the company with it.
Post Script: You literally have demon in your forum name. By your own logic, you're glorifying the biggest evil in Christian religions. While I'm not particularily religious myself, I'm sure someone who is would be perfectly happy in throwing your words about glotifying something vile right back at you.