I also generally recommend not writing IF stories in such settings. 
I have talked about this in several other places, but my main point is that realism does not inherently make a story good, especially if that realism is mainly being used to hurt minority players.
I’m not saying you can’t include bigotry in IF games, but if you do, it should be targeted at the character, not the player, and either all players should face that persecution, or the choice of whether to face persecution or not is unconnected with things like sexuality and skin colour (I understand that this is how Choice of Rebels handles it). This is especially true if the setting is fictional (if you’re making your own setting, you can definitely choose exactly how much bigotry there is), but it’s even true for settings based on more bigoted places and times in the real world.
For one thing, what we think of as “realistic” is often incorrect. For example, in the Middle Ages, both Christianity and Islam were far more tolerant of homosexuality than they are even today in some places. And even in places and times where there definitely was/is such persecution, you’d be writing a whole lot of extra story which would only really be encountered by players who wouldn’t really like that content, so why not just make it more accepting? You’re definitely going to be going against realism in other places; it’s pretty much inevitable.
Also, I hope @Flashe doesn’t mind, but I changed the subforum to Writing and Content, because this topic didn’t really fit in ChoiceScript Help.