What? I really don't see how the transsexual horse is meant to be offensive.
But regardless, even RTD threw in jokes about sexual minorities, hell he even used the word "gay" as a pejorative. After the first time he did it (Aliens of London, Rose describes Jackie slapping the Doctor as "so gay") people actually accused him of being homophobic(!) because of it.
I have googled both scenes, the one you mentioned too and rewatched them.
First the "transsexual horse":
The doctor says "I speak horse. He's called Susan, and he wants you to respect his life choices."
In general it makes a difference if it is a gay person, who makes a joke about being gay (or other sexual minorities) or a straight person.
And gay people notice the difference. We know, if and when we are included in the audience or not.
Yes, I believe that Moffat didn't/doesn't have bad intentions when he writes stuff like that. But it's soo incredibly dumb, heterosexual, stale and very "yesterday" nonetheless.
So, being transsexual is a choice? And shouldn't the - so accepting doctor - say her, not his?
And it's even dangerous. In the USA religious lunatics also believe that being gay or being transsexual is a "choice" for a "lifestyle" with devastating results for young gay/trans people.
Moffat's humour is a kind of humour that excludes sexual minorities from the audience. It is laughing about, not with trans people. "Her name is Susan and she wants you to respect her identity" might have been something that trans and gay people might find funny too (which would still be generous).
But it was just one example for Moffat's male hetero-centrism. And I don't say that he's a homophobe, he's just narrow-minded.
Now the other scene.
Totally different thing for me. It was a remark from a working-class girl, not the superiour 900 year old being. I don't feel offended now and didn't object back then. And if people called RTD a homophobe - where were they, when Susan was on screen?

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