Having worked in the publishing industry for a few years I feel I can quite confidently say that this kind of thing happens ALL the time. The agent in question may well have nothing against gay characters in a book, but they may think that editors will have a problem with it, and the editors may think that Sales & Marketing will have a problem with it, and Sales & Marketing may think that bookshop buyers will have a problem with it, and bookshop buyers may think that customers will have a problem with it. You see the issue here? Everyone trying to second guess everyone else. The status quo is maintained.
Here's my plea: ENOUGH WITH THE SECOND GUESSING. Give people a chance to make up their own minds. Simple.
I have a great deal of respect for the two authors in question for refusing to 'straighten' their gay character. I reckon a lot of writers would feel they HAD to, in order to sign with an agent.
So what about you? What would be your deal-breaker? What would you do if you were asked to change the sex/race/sexuality of a character in your manuscript?