So is Alistair doomed to hate male warden?

Alistair definitely dislikes a male Warden who ends up king consort married to Anora. However, I don't think he has any issues with other male Wardens. I've only played as male twice, though. I think there might be an import bug where Alistair thinks the male Warden dissed him even in cases where he didn't. Probably your best bet would be not hardening Alistair and picking Anora for queen on her own.

Yeah, it's more like Alistair has a problem with living Wardens in general (except when romanced).

After all, all the options that allow the HoF to survive involve something Alistair hates. Either doing the Dark Ritual or sparing Loghain.

That's what I don't understand: in DAI he talks bad about ANY GW if dark ritual was performed and if your GW isn't in romance with him. So actually it is, as it has been said, a poor writing.
Alistair in DAI is just a hypocrite: dark ritual WAS and exactly Alistair was involved. But if your GW is in romance with him - he tells only good things about your GW, but if you are not in romance with him (but were even very good friends)- you hear this shit about your own GW, the GW who helped Alistair with his family matters, who listened to him and didn't make Alistair a king, who fought side by side, was a good friend.
Male or Female GW - doesn't matter at all, you still hear that "dark path, I wouldn't count on her/him blah-blah" considering the fact that he himself agreed to sleep with Morrigan (yeah, thanks a lot, stupid whininning Alistair for kind words after all we together have come through).
Don't know why it has been done. Poor writing? Sloppiness? Or on purpose to show him a hypocrite? Never will know.