I'm not a fan of fiction that feels the need to treat its characters with kid gloves lest the writers be perceived as catering to some sort of stereotype.
Granted DS9 went a little overboard with the "Gays only exist in the Mirror Universe!" cliche, but there's a huge difference between a single incident involving one character and multiple incidents with multiple characters.
IMO if you really feel that the writing of Sisko is catering to a stereotype you're not giving the writers enough credit.
I'm not saying that the minority characters have to be treated with kid gloves. I'm saying that you have to take the cultural and historical background into account when dealing with them in certain situations. These characters, intended or not, can be looked at as role models. Whoopi Goldberg said that she got into TOS because it was one of the few shows that had a woman that looked like her that wasn't a maid.
When a young black boy sees Ben Sisko as a role model who then leaves his family, leaving a single mother, does it simply reinforce the idea that that is proper behavior for black men? It doesn't have to necessarily be shown that the father is leaving of his own free will. Just the fact that he's leaving can have an effect on someone. The writers of the shows (and books) have to be aware of this and take it into account when deciding on storylines. That doesn't mean that you can't have it happen but, as Avery Brooks said, you have to look at it with a more critical eye.