I was displeased with the lines from The Iron Bull regarding Krem. If he wants to think of Krem as a male, that's fine, but he is in direct conflict with the Qun. In Origins, Sten confirms that children are assigned numbers and symbols at birth, raised by the Tamserans or whatever, and then assigned their roles based on their observed aptitudes and talents. Sten also states that no one can change who they are. A baker cannot be a warrior. A farmer cannot be an artisan. And so on. You can't tell me the Qunari would ever think a biological female could ever be a male, which is what The Iron Bull claims to be the case. He doesn't say females can become warriors under the Qun, he says they become males in order to be warriors. That would completely contradict what Sten said in Origins, which is why I hand-wave this as The Iron Bull making stuff up for Krem's sake. The Iron Bull strikes me as the type who doesn't truly believe in the Qun to begin with.
As for the issues brought up by the OP, I agree. Having the choice to be prejudice should be included. Even those who always choose the tolerant option have to agree with this, because without the option to be prejudice, the choice to be tolerant means nothing.
Example:
"My Inquisitor was tolerant of Krem's identity and supported him!"
"So what? Everyone's Inquisitor was tolerant. There was no other choice."
See what I mean?
And yes, Thedas has prejudice. It is seen everywhere. Against elves, against dwarves, against humans, against qunari. And then there is prejudice within those races, against mages, against templars, against Orlesians, against Fereldens, against Tevinters. The white and black chantries. Between dwarves with "stone sense" and surface dwarves, between caste dwarves and casteless dwarves, between Orzammar and Kal'Sharok. Between Dalish elves and city elves. And yes, against non-heterosexuals. In Origins, a male Warden had some colorful ways to turn down Zevran's advances, responses that prove some societies outright hate alternative sexualities.
So I agree that BioWare needs to remain consistent with Origins and let players choose how their character respond to such situations. Player choice.
I think the problem is that BioWare has marketed to certain populations that define themselves by their sexualities, and now those groups expect BioWare to promote those sexualities in their games. BioWare may have just painted itself into a corner. But David Gaider, to his credit, has said that no storyline should be off limits. So who knows where they will take this? I say side with player choice.