Interesting enough, this is a good conversation on religion and inclusion/exclusion and would make a great topic in general for the boards. That said, I agree with @Autumn, if there is a recognizable substitute it won't be heard for those looking to make argument to argue. Regardless, people will be offended. Even on space games, once someone can make the reference to something real world, arguments can be had. No different than some conversations on early Dune games.
Oddly, I don't see this much on WoD games (pub debates) that do take various religions and play 'bad' entities or monsters associated with them (and are usually nipped in the but with staff warnings when I do see them). Thus, I am guessing it comes down to history and the perception of wars mostly being religious in nature, despite most evidence pointing towards resources (namely land, or resource rich land) as the main factor for warfare. I don't want to get into misperceptions of modern warfare at all (and I am a veteran of the first gulf war, I have lifer friends who have spent years in Iraq and Afghanistan on the 'close to home'/first hand/second hand front to avoid that being a discussion).
This all being said and having discussed it with current staff on the game, we're still following the alternative history approach. It can be viewed as alt earth in that we are only taking the idealistic approach to the main religions and their aims at well being of the people over any human misinterpretation (that leads to the murder/rape/genocide).
We will be following the nip in the butt plan. We have initially set up a warn/ban policy for the game from the get go (one warning, repeated behavior is ban); we do this on Coral Springs and have banned, peace is being maintained (though smaller player base) with no tears spilled over any bannings to date. We are strongly agreeing that most people have learned in kindergarten or early learning development centers about respecting each other and sharing toys and playing nice, no excuse in not being civil.
We are setting up a policy to cover religion, limiting any talk on religion to a religion channel, with the caveat that should discussion on this chan become heated staff can shut it down. Along with a policy of gagging anyone who may push religion on other chans such as pub, leading to warns/bans for repeated offenses (buffers will be on, if staff misses it, others can report it certainly). We are including in the policy that IC portrayal should not be one of intolerance or hatred and it will be not be allowed (warn/ban) with an inclusion that should anyone say they are uncomfortable with a portrayal of any minor intolerance, the RP should be stopped. And repeated offense of the same nature will lead to following our warn/ban. As of now, this is the largest section of said policy.
Another thing we are working on is to establish the religion pages before we are ready for CG (one mistake with Realms). This is to define the teachings/ideals of the religion (love your neighbors/the five pillars/tolerance). Doesn't mean a certain disliked character may skirt these a little, but this is outside the norm and will be monitored, applications towards religious will be scrutinized (not discouraged).
We feel the time period offers enough potential by way of politics and conflict without evoking religion, along with the potential birth of a nation in the face of conquest or the assimilation into another culture that one views as better than say the feudal ways of the old kingdoms, that it is good. If we redefine or reface by calling it alt earth, it doesn't remove the potential for said debates as have been outlined.
And yes, religion became a debacle on Realms, despite staff adhering to the idea that Christians and pagans alike practiced tolerance in the face of numerous enemies at the gates so to speak. And as has been pointed out, people still pushed the topic, making some extreme comments on religion. Mostly not serious, the context was lost many times on pub channel comments. The worst being pagan debates, despite Madoc and myself saying both views were welcome and without a hierarchy, both could conceivably exist.
This may nip me in the but at some point (Cirno insisting I am racist with the no-foreigner policy), but we are really after alternative history at this point and have a strong liking of the period in question.
Sidenote: yes, we are clearly defining styles of dress, styles of homes, and other cultural aspects more clearly up front to avoid debate in deviation between centuries of time.