Boy in ballet, he must be....learning to dance?
It's always difficult to counter these types of comments. Does one start with the assumption about sexual orientation, or the idea that being effeminate or homosexual is somehow wrong?
Personally, I like to go with deliberate, cheerful ignorance. Most people, when asked to actually clarify what they know to be an uncharitable assumption or insensitive statement will realize they're being inappropriate and put a lid on it.
Them: "Your boy's in ballet? Do you want him to be...you know?"
You, smiling: "Know what?"
Them: "Well, don't you worry he's going to turn out..."
You, still politely: "Turn out how?"
Them: "Um, gay."
You, looking pleasantly confused: "I can't see how a dance class would affect that. Besides, it's not like it's a bad thing."
And then go right back to what you were doing, or go grab a cup of coffee, or make some copies.