Hmmm....we talk about things like this a lot, though I'm not sure, not knowing specifics, about the example that you bring up.
We've encountered people we know and like or people from places that we know well and like being homophobic and have explained much of this to Q. Generally, we talk about peoples' different beliefs and what I see as the nuance between those folks having those beliefs and me/us believing they are wrong because they are hurtful to people, discriminate, seem to think that hate is okay, etc. We talk a lot about being queer as an identity and how it's not okay to discriminate based on any identity. But we have also recently talked some about how some people's religion tells them (or folks interpret their religion as telling them) that being gay/queer is wrong. Q recently said, "If Jesus were really god, he'd say it was wrong to hate gay people." Or something to that effect. I've explained that, as a non-religious person, much of what I understand about Christianity in particular is about love, care, and openness, and how that doesn't jive with not accepting someone's identity.
I think the layers of this get deeper and deeper as kids get older.
So, I'm thinking I'm perhaps not answering what you're asking. Bottom line is that I try to explain a belief or stance, explain why it is different than our belief or stance, and then try to be honest about the effects of those beliefs on me, our family, etc.: "It really hurts me or makes me mad when...." "I don't think it's right to say this about certain groups of people..." "I don't have the same belief as X....and in fact that belief is hurtful to me because...." I'll admit that sometimes I also just say, "...and personally I think it's wrong or hateful to have that belief." (maybe that last bit is wrong of me, but heck, it's what I believe, right? (hoping for no flames here....)
Hoping this might help a wee bit....