Frankly this should be taboo for decency reasons alone!
freedom of speech protects against this type of censorship (thankfully) . Im guessing they used religion because they have used a ton of other stuff, and wanted some new ideas, and this is one that the R/D guys came up with. i wouldnt label it as a "religious shooter" personally, however It certainly uses a religion driven antagonist group, but thats not All the game is about. I think your looking too deep into it with an anecdotal viewpoint (which is your right). I watched the entire video, and I think it looked great.
FC games have had religious components to them, FC4 had Buddhism, Hinduism (in a vague sense) but it had a definite religious part, but that didnt define the game, and certainly didnt make it a "religious shooter".
Far Cry 3 used indigenous religions of the Pacific Asian islands , i.e rituals, (and other stuff i dont recall perfectly, but i do recall it had some content that could be seen as religious) even the ending could be interpreted as a religious person defeating their inner demons.
Far Cry 2 had what I would describe as Political/Social factions (which most ofthe FC series seem to contain) and many could say politics is equally as "taboo" as Religion.
IMO, I think its always best to allow freedom of expression , and since the Supreme court has decided that Video Games DO fall under the protection of the First Amendment (right of Free speech) video game creators are allowed to enjoy that freedom to express themselves without worry of persecution . IMO suppressing Any form of artistic expression can only serve to hinder creativity, and really only insults the population of a given society (essentially a government or ruling body deciding what its people can or cant be exposed to is simply patronizing, and silly IMO). another reason im thankful to be an American, and to enjoy the freedoms afforded to me.
Edit
Just to be clear I do respect your opinion that it's not decent, & i'm not arguing whether I do or don't condone certain content. What I am arguing is that I believe in the right of freedom pertaining to artistic expression. There are many things I find offensive personally but I defend the right for those people to express their opinions regardless of whether or not I personally approve.