I really didn't want to weigh in here. The premise of this thread seems to be that a playwright has to dumb down to the dumbest members of his audience. And this seems a completely invalid approach to a play like ANGELS IN AMERICA, which the dumbest members of an audience have no chance of even beginning to appreciate in any event.
Having said that:
Like many people who seroconverted in the 80s, Roy Cohn did not survive.
Like many people who seroconverted in the 80s, Prior survives. How long we don't know.
Like many people whose lives intertwined with people who seroconverted in the 80s, the rest of the characters in ANGELS do not contract hiv.
As has already been noted, ANGELS IN AMERICA is not a tragedy, it's a fantasia. A mythic epic.
Prior is a modern day Jacob, who wrestles with the angel and is reborn, not as someone who will necessarily not die of AIDS, but, metaphorically, as someone who like Jacob is renamed. Jacob became "Israel" which means "perevereth with God."
Finally, there is nothing in ANGELS IN AMERICA that suggests that right wing assholes die of AIDS whereas drag queens with good hearts survive it. To think such a thing or to consider that others who might think such a thing should be pandered to with a different ending is frankly silly.