Lefey was saying that she suspects CC was having a joke with us slashers with the kiss in the RatB, but you know, I doubt that very much.
I haven't see the Lone Gunmen series, so I don't know what kind of homoerotic jokes they had there, but I've always thought CC had a slashy mind and it's difficult to think of him as being actually homophobic.
It seems from many of the lines and the way the characters have acted, CC has always left room for slashy potential. I think he really had fun with the RatB and would have pursued the M/K relationship if viewer response had been favourable. ie. if the majority of viewers were slashers, our views would have been more easily reflected.
Of course another thing that might have prevented the story from developing was the inavailability of Nick since CC reportedly is famous for being a control freak.