They're an ethnic group more than a religion. I don't know of any Jewish-Samaritan conversions and they certainly shouldn't be a heresy.
If they had had a much larger historical presence, I'd have made them a separate religious branch of Judaic (formerly Hebrew), and converted a couple provinces in Israel to it. But even then there's no way to provide them holy sites that are both realistic and balanced.
Thanks for all of the help with the mod. I've been able to do everything and keep my game going. I'm now toying with the idea of adding some stuff of my own. I'll let you know how that goes. Out of curiosity, can the holy sites be weighted in any way? For example, Jerusalem should hardly carry the same weight as Sinai, Semien, or any other Jewish holy site for the matter. Same for other religions.
I just wanted to add that I think I can help you with the Samaritans. They're not really an ethnic group per se, although I suppose they could be defined as such. To put it another way, if you'd consider them an ethnic group then all the Jewish sub groups would end up with that definition (eg- Ashkenazi, Mizrachi, Sephardi, Beta Israel, Kalimi, Bukharan, Mountain Jews, and a bunch of others.). OTOH, Judaism itself is a ethno-national religion, so Samaritanism can be defined the same way.
However, the Samaritans are genuinely separate from Jews in the practice of religion, albeit with a lot of overlap. Most importantly, they were a very sizeable community--perhaps larger than Jews--in the 6th/7th centuries or thereabouts. Granted, this was right before the game time frame, but Muslim leaders still feared Samaritan revolts enough to continue intense persecution of the Samaritans into the 9th or 10th centuries, perhaps later. This is a strong indication that they maintained a still sizeable, if much reduced, presence into the centuries preceding the High Middle Ages. If you'd like I'll check my library and see if I've got any handy sources that cover this information. In any event, while I understand why you removed them, I disagree with your reasons for removing them, save for the point about holy sites; I cannot dispute that being a problem.