Both of the those examples are actually red-herrings. Their true cause is not religion, again both of those situations are simply politics utlizling religion to galvanize the common populace into acts that support the political agenda of the ruling elite.
The problems in N. Ireland began with England's partitioning it off from the rest of Ireland when they granted Ireland home rule. Subsequently, Ireland and England played upon religious themes to exacerbate the political disunity. Ireland doing so bcz they wanted to make it become so inconvenient for England to maintain N. Ireland that they'd simply surrender it to the Irish. England bcz they wanted to demonstrate the necessity of keeping N. Ireland, that is, bcz they need to protect those poor protestants living there. In truth, if N. Ireland had been awarded to Ireland back when Michael Collins negotiated for Irish home rule, then nobody would be fighting, and neither the catholics nor the protestants would even think about each other.
As to the KKK, well, this should be obvious. This resulted from an economic necessity of maintaining slavery. Politically, slavery had become unpopular in the enlightened world (largely, it should be noted, bcz of Christian activists arguing against the immorality of such a practice), hence the ruling elite of the south needed to create a system of justification for slavery that would inspire the poor white southerners into fighting for its continued existence. The easiest tool for achieving this goal was to bastardize religion into something that might look like it could justify slavery. If anyone has seriously examined White Supremacy websites, one must be struck by the entire lack of any cogent thought in regards to its use of religion. In fact, the irony of these streams of thought is that the entirety of their scriptural references derive from the Jewish Old Covenant; nothing from the Christian New Covenant. In effect then, they are using Judaism to advocate anti-semitism. It's like they converted to a new sect of Judaism, and then decided to hate other Jews who aren't part of their sect. BUT, they have, to some degree, become Jews themselves. At any rate, I digress, the point is that the fundamental reason for the KKK's existence has nothing to do with religion, religion is simply a tool which it employs to stir the emotions of the masses. The true reason for the KKK's existence is centered around its politcal attempts to maintain the economic system of slavery.
Anyways, my point stands. Just because a civ isn't popular or well known isn't a reason to disclude them. Perhaps it's a reason to choose another civ before that one, but not a reason to completely eliminate them. I would like to see 75+ civilizations in future Civ games. 
