First I want to say that I agree with you but there is one point that I think they treated more subtly than you describe here. When Sal was fired it was not, imo, strictly for not entertaining a client. If you recall, Don first discovered Sal was gay before the incident with Lee Garner. Don's response at the time was to tell Sal to be discreet. My reading of this was that Don, perhaps somewhat anachronistically and certainly out of character, did not have a problem with Sal's sexuality but understood that it could cause trouble for Sal and maybe even the firm. So when Lee demands that Sal be taken off the account the firm has no choice. Lucky Strike pays the bills. Also, you might recall that it was Roger who fired Sal not Don. It was Roger because Lucky Strike was his account and Lee only dealt with him. Roger didn't even care to know the reason. IIRC he even said something to the effect of "Lee wants you gone so you're gone. It doesn't matter why." Don's response to this was the privately tell Sal he'd be a reference for him. My recollection of that episode was that Don had little to do with the outcome and was uncharacteristically compassionate.

If my read on this particular scene is accurate I think it does actually further prove the point you're making. The show did go out of its way to make Don a more sympathetic character to a 21st century audience despite him being a real piece of shit.

Edit: another way to read Don's acceptance (if you could call it that) of Sal's sexuality was not that he was ok with being gay but that he understood what it was like to have a real secret. He understood what it means to live a lie and present yourself as someone you're not. This maybe allowed him to refrain from judging Sal even if he did have a problem with homosexuality.