It seems odd to me. Paradox is a Swedish company, and Sweden is a fairly liberal country. Same-sex marriage was legalized in 2009, and even the Church of Sweden gave the go-ahead on performing same-sex marriages the same year. The game logic around this is simple enough that changing two byes fixes it, so it's not a technical issue. What gives?
Presumably slavish dedication to historical accuracy. Although were there really no cultures in that era that allowed same sex marriage? I personally wouldn't want a seemingly historically accurate (ish) game to present the churches of the age as being okay with same sex marriage when they weren't. Although being able to toggle it on in the settings would be cool.
No Christian cultures, obviously.