do you think that don would had been more supportive of sal if he hadn't seen the partially undressed bellhop in sal's hotel room?

I'm not sure homophobia has anything to do with it. One of the young copywriters (Kurt?) is openly gay, and Don hasn't found a reason to dump him.
I think Don's main problem was that Sal didn't limit his exposure. His exposure, and subsequent rejection of Lee Garner Jr. led to the potential loss of a major $25mil account. Much worse in any businessman's eyes than who he schtupps.

I think of a homophobic person as one who is horrified by homosexuality, makes fun of it, derides it and avoids it.  I don't see Don quite in that category.  He lets Sal keep his secret after the out-of-town trip and while not exactly sympathetic to gay causes ("you people," he says), he is worldly enough to know it's out there and not going away.  Business is far more important than any sexual behavior (see mneeley above).

I'm still not convinced that Don meant gays when he said "you people". I was thinking he might have meant, "You people that don't get the dog-eat-dog nature of business and create big problems for me from your petty problems."  I guess I thought that because Sal is part of Creative, and Don is moving out of sympathy with that department, as he's been forced to up his game since dealing with the Brits and Connie.  I really don't think that Don cares one way or the other about Sal, beyond the reflexive distaste that comes from the conformity paradigm of the early sixties. I think Don even has personal sympathy because he identifies with the hidden identity.  But he is getting harder, more cynical, when it comes to dealing with colleagues this season!

I agree, nothing about the writing of this show to date has been particularly superficial and I think there were layers to what Don meant by the term. In fact, I read it as linking up to what he has had to repeatedly tell Peggy and his jr. execs - that they have to work harder and stop asking for things.
In Sal's case, if Don were homophobic, we would have probably seen it in his reaction to what he saw at the hotel - either immediately or in the plane thereafter. Given his gentleness then, my guess is that Don was more bothered by Sal's coming in to his office to try to get Don to "fix" the situation rather than figure it out & survive on his own.

I read that as a "do what you have to do" line... that he expected Sal to compromise his personal integrity for the business.  It was kind of a strange position at the time, since I gather it was a heterosexual male-dominated business.  Sex didn't often enter into the equation outside of the host simply "providing" some women to entertain their guest.  We could question if Don would expect the same of himself, and his past behavior seems to indicate he's willing and ready to set up more-than-just-business relationships with the powerful women who come with accounts (Rachel Menken, Bobbie Barrett) - but he was attracted to them anyway (who wouldn't be?) so that doesn't really count.  The only other person who may face a comparable situation to Sal is Peggy, and she hasn't really faced that yet... her stint with Duck was suspicious though.  Sal, on the other hand, is not as comfortable with his sexuality nor with being unfaithful to his wife (although to what extent this is a cover for his insecurity I don't know)... let alone anyone even wanting to let that tobacco creeper within touching distance.

Oh yeah, and I don't think Don is homophobic.  But he is a morally ambiguous man, and expects the same of others apparently.

I don't think Don Draper is homophobic. I also don't think it was ONLY a coincidence that Sal was told "do what you have to do."  Yet Conrad Hilton scolded Don for not including Hilton on the Moon. Both Sal and Don resisted the client. The weak character was jettisoned, the powerful character was not.