Representing religions in game

I think it might be a bit too controversial to make a game about religious prosecution since I assume some players would be doing the prosecuting?

It might be better to go with something a little different in which people can still recognize that conflict.
People tend to be fine with playing the german army in games, their army did look rather unique and stylish after all but they wouldnt want to be building the concentration camps, rounding up the jews and such.

So yes, I'd advice going with a metaphor, or going further back in history.

Romans prosecuting christians could work perhaps, and might help to open some eyes considering how christianity later prosecuted others.

To avoid controversy, a metaphor could be used though, like seen in the movie Equilibrium. Where the world is made orderly and emotion is banned, where those with feelings are prosecuted.
Something similar with an opressive regime and a rebellion could work.

With this, I would definitely avoid the subject of religion. It's far too much of a hot topic and no good can come of it unless it's been done extremely well.

I would leave religious topics to those with a deep religious understanding and historical knowledge, and even then it would need to be tempered by a lot of common sense (which is rarely common) and political correctness to avoid major outrage.

There are many games that play on controversial issues of the day, but rarely do they succeed when talking about more recent events (within the player's lifetime). Twilight Struggle, however, managed to create the proper atmosphere with the Cold War, but it did a good job of not portraying either side as right or wrong.

With your particular game, I recommend that you follow a few guidelines so as not to offend those of the religious persuasion (such as myself, though I'm not easily offended. As an aside, I'm actually somewhat of a scholar of a variety of religions, so you can PM me if you have questions on anything).

-Avoid mention of specific religious figures(example, any mention of the Pope, of the Prophet Muhammad [Peace and blessings be upon him], of Jesus Christ, or other religious figures of prominence in scripture or of our day, should be done with the utmost reverence).
-Try to avoid events that a religion actively avoids discussing (I'll refrain from mentioning any here out of respect to those organizations).
-If the game is about a controversial event, make sure that you, the designer, thematically approach it from neutral moral ground (it's very easy to make the mistake of casting one side as "the Evil Empire" a la Star Wars).
-Be careful what you ask the players to do - if one side is supposed to do something that strikes the player as overtly wrong, the game stops being about fun and starts to be a documentary.

That said, is your intent to make the game an example of investigative journalism? Judging by your posts, I'd say that's not your intent. However, pointing out class struggles with animal markers and showing inequality in the player's forces isn't bad design, but if you do couch it in a religious/period theme, be careful in your presentation thereof.

The sort of outrage you are talking about tends to be more the domain of religious fundamentalists, like evangelical protestants or what Biblical Christians would call "cultural Christians." If you want a good slice of life, look up Donald Trump's evangelical advisory board. Unless you are designing the next "Apples to Apples" then you really don't need to worry about their input. They tend to aggressively protest products that none of the individual members have actually seen or used, and baiting them has become something of a marketing technique in and of itself, seeing as how the negative attention from a group that isn't part of your target demographic to begin with generates inordinate media coverage and positive buzz among your intended consumer base (for example, look online for footage of Kevin Smith protesting his own movie). Any game designer should be so lucky!

Likewise, I doubt ISIL will track you down for doing an analogy of Abdul Hamid's 1894 government instituted genocide against the Armenians. That said, it is still a hot topic in Turkey to this day in spite of Adolf Hitler's statement, "Who, after all, speaks today of the annihilation of the Armenians?" when justifying his own genocidal campaign.

In terms of your notion of representing various persecutions in history and why it would require some delicacy, my mother and grandparents were held in a concentration camp (not a death camp) during World War II, and I have friends who were persecuted by the SS, so genocide and persecution aren't intellectually removed topics for everyone. Just look at what is happening to the Jews in France today. So, in making a game of such things, which animal runs the Bosnian rape camps?

I do get a little edgy when someone handles the topic of genocide in a ham-fisted way, and I no longer consider it ethical to play Nazis in games. It's really not so much a matter of religion for me, seeing as how my family was persecuted for being Slavs, just as I have relatives who suffered under Stalin's regime. Rather, in most instances, I see such attitudes in the U.S. as symptomatic of privilege and the social concept of "whiteness," which is to say that it is easier for someone who is far removed from torture to write a game about it than for someone who has the experience in their orbit.

I think Willem Verheij's comment sums up what is irksome for the general 'religious' community: "Romans prosecuting christians could work perhaps, and might help to open some eyes considering how christianity later prosecuted others." Elementary simplification like that is . . . just . . . so . . . tiresome, even if it makes for great pop culture and fundamentalist-type rhetoric. Persecution throughout history is a rich and nuanced field of study, and the motivations for such acts are by far more a matter of geopolitics and economics than religion, even if the pre-Enlightenment landscape is somewhat unfamiliar for modern audiences. I do find it distasteful when people turn historic persons into caricatures, whether out of simple ignorance or to better fit their own ideological framework.

As to what animals represent what religions. Sheep are an accepted Christian analog. Camels are closely associated with the Middle-East for a general audience, and there is mention of Muhammad conversing with them and expressing fondness for his own in the Quran (although you would want to keep aniconism in mind). Judaism is tricky, because the lion and dove have been appropriated by Christianity, and then sacrificial animals, like the ram and bull, are respectively associated with paganism and transgression. I really can't think of one that is identifiable in the popular conscious. Cow for Hinduism. Definitely the eagle for Tengrism, which would technically be the religion associated with the most profound genocides. Of course, leaving out communist ideologies, exempts the massive body counts under Stalin or Mao, the latter of whose policies alone killed more people than any single religion's ascribed sum total. Maybe the bear to represent general atheism?

Feel free to PM me if you have an interest in the subject, as historic inquisition was a field of study for me in college that I have great interest in and can make several good reading recommendations regarding.