Yes, RTD (Davies, the Torchwood creator) has pretty much admitted he does have a gay agenda.
That being said, Harkness is supposed to be pansexual, meaning he’ll take anything (even worse then Kirk). But fans have noted that this season he does seem exclusively gay.
I don’t read the theme as being “a gay man saves the world”. But I can see how people take it that way.
And of course, a cool piece of trivia is that Torchwood is an anagram for the parent show. Which restarts in 4 days. I (and 5 kids in the subdivision) cannot wait.