You start falsifying history the moment you unpause the game. Equality shouldn't be there at the start of the game, nor the most common outcome, but there is no reason the game engine needs to forbid it.
imho the thing to do is take OPs suggestion, Paradox should make gay-marriage possible but have people refer to it in variable ways. Some egalitarian societies can call it marriage, others sodomy, etc. And then add other cross-cultural restrictions too, where civilizations may not recognize bi-religious or bi-racial marriages for various reasons.
In other words don't minimize the issue, lean into it in a CK way, deeply and unsettlingly.