If you make it equal, you remove the drama. If you force equality onto history, you falsify it.
Case in point: Edward II, king of England. He had affairs with Gaveston and Despenser the Younger, all the while in a marriage with queen Isabella. He wasn't too subtle about what he was doing, showered his lovers with gifts, prestige and land. His nobles pressured him send him away, but he was the KING, and it went back and forth a few times.
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.
Not equality of people, equality of paths. In an FPS the shotgun and the rocket launcher shouldn't be equal or there's no need for both.
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.
There is also an extensive modding community. There's no reason Westeros or post-apocalyptic North America needs to have the same attitudes towards gender and sexuality as medieval Europe.
If you make it equal, you remove the drama. If you force equality onto history, you falsify it.
Case in point: Edward II, king of England. He had affairs with Gaveston and Despenser the Younger, all the while in a marriage with queen Isabella. He wasn't too subtle about what he was doing, showered his lovers with gifts, prestige and land. His nobles pressured him send him away, but he was the KING, and it went back and forth a few times.
If it's in game, it should be called "sodomy".