The problem I see with this is that somebody somewhere is going to take offense to it. There was a time when things like Captain America punching Hitler in the face was okay, but these are not those times. Personally I see nothing wrong with it, and I also feel that our world is a little TOO Politically Correct. And I'm sure I'm going to offend somebody even by saying that. I just don't see this happening. As long as it is kept in Fictionland then it should be fine. However, you start using real world groups and religions and somebody is bound to start screaming bloody murder about it.

Crazy religious radical groups are bound to happen anyway. They appear in pretty much any superhero or fantasy setting.

Depends what you mean by crazy religious groups. The Banished Pantheon were a crazy religious group. The CoT weren't so much, but they pretended to be exercising their constitutional right to sacrifice pretty girls on street corners.

City of Heroes had the Banished Pantheon whom caused a zombie apocalypse that killed off the entire population in one of the zones (if I am remembering this correctly). I think Circle of Thorns was more of a mage sacrificial group then...they might of been more interested in magical entities then anything else but I am not sure if that is much different and I can't recall that much about them other then the fact that they loved to summon demons and wraiths.

Now I wasn't saying the crazy religious radical groups are needed in every fantasy/superhero game. What I was saying is that it's quite common for that to appear in those type of games. Foradin only got a chunk of the ones I have seen. WoW also had the Burning Blade Cult and the Twillight Hammer. CO I think had a militarized snake themed faction that had some snake cutlists in it who did summon a minion of a god at one point to kill you (I think). AoC definetly had some necromancer cults (although I don't know there names) both Guild Wars games had the White Mantle.

They are a quite common enemy to see in games and it's not hard to see why...considering real word history and all. The only real issue I would have if real world radical religious terrorists were used in the Mission Creator is if the author were to present it like every person of the religion that terrorist faction belonged to was a radical terrorist themselves. I have a serious problem with generalizing and brush stroking a group of people as the same.

My gut says that a Dev will either ask you to change it, or remove it. As I've said, people are awfully touchy today as compared to several years ago. For liability reasons I'm fairly sure that is what will happen. If ONE person deems it offensive enough there could be a law suit involved.

I think it's fair to say that it is plausible that CoT will have Diety lore.. but I sincerely doubt it's tied to current earth Theology

Considerably more harm than good will come from integrating real-world religion and/or politics with CoT.

It'll happen. Some of it will be in the game. Some of it will be player created. Some of it will be ok. Some won't. It'll be handled.

Just like CoH.

I think we should be allowed to use any political or religious group, so long as it's clear that the Villains are a radical splinter group and do not represent most of the people who subscribe to the same beliefs.
Unless they're all robots or monsters, every villain has to be some race, so it's not racist to show a villain of any particular race, but it is racist to imply that all members of that race are villains. The same rule should go for beliefs. If we want our villains to be realistic, we will give them motives drawn from a realistic set of beliefs. Naturally since they're villains those beliefs are going to be a bit twisted in their heads.
Adventure stories are just like any other kind of literature. They can be springboards for discussion about philosophy and religion. The Superhero Genre Is About The Struggle Between Good And Evil. It Deals With The Mysterious And Miraculous In A Symbolic Way. Anyone Who Doesn't Realize That Superheroes Are Really About Religion, Just Isn't Paying Attention. I don't take offense or assume the author is anti Catholic just because a villain in his story is a priest. But I would be offended if the author implied that every priest, was just like his villain.

What follows is an excerpt from a pen & paper game I'm making:

Most most common criminals just want to make money, They steel things they smuggle stuff and they stockpile weapons to protect their interests but they don't usually have any interest in taking big risks or making statements (unless it's aimed at eliminating competition). Ideological groups on the other hand, are really into Grand Schemes. So naturally if you want to make a great super villain, you're going to want someone with insane ideas.
Of course, twisting realistic ideologies into villainous parodies or pushing them to radical extremes, runs the risk of offending lots of people and besides that it takes a lot of work. EG: If you want to use communists, you need to think about what a communist villain would want to do, to advance the cause of communism. Fortunately there are several popular comic book villain ideologies that don't have to make sense. An Anarchist doesn't have to believe that killing the mayor will advance his cause, he just wants to shake things up for the sheeple.
Insane as they are, these are still beliefs that some people in the real world have held, and they always have terrible consequences; so you can easily picture mindless minions being drawn to a charismatic leader of these kinds.

ANARCHISTS
The most appealing of these. Anarchists love freedom, hate authority and want to do away with government. Any attack on Government or large industries might come from anarchists.

NIHILISTS
Nihilists are more pessimistic, they don't believe in freedom. They just hate civilization and want to do away with it. Like Anarchists, they often target governments or big businesses but Nihilists are also fond of attacks on large populations.

ELITISTS
Reveling in pleasure and power, Elitists see themselves as superior to ordinary people and privileged to do as they please. They might style themselves after some royal family of the past, or they could be radical racists, but many Elitists simply base their belief in their own superiority on some source of power that they posses. They could be intellectuals with high technology, mutants with a variety of powers, or even vampires.
Elitists often want to conquer (not necessarily the world) but sometimes they already rule a secret empire of some sort and just want to protect their interests. EG: keep their secrets, traffic their contraband, lure their victims etc...

SATANISTS
Unapologetically rallying around a symbol of evil, satanist, hate good. There are 2 basic types of satanists. Radical atheists, who hate religion, and lunatics who worship an evil spirit in hopes of gaining some pleasure or power. Both groups might attack churches, but only the second group will try to sacrifice people so they can summon a monster.

NAZIS
Nazis are just one type of Elitist but they get special attention because they've played a big role in comic book history, just as they did in real history, But WWII was more than 75 years ago. They're no longer a serious threat, and using them just doesn't make sense any more. but they can still hurt people's feelings, so just don't use them.