I shot up Gomorrah, and the Side Bets quest instructed me to tell Yes Man the Omertas are now hostile with me. But when I talk to him my only option is to ignore them, and I don't want to do that because they're bastards.

Also, according to the wiki you're supposed to be able to change your opinion of a faction, but I can't shift the White Gloves from ignored to positive. That may not actually be possible, but it seems worth mentioning.

Yes Man is still in front of the Tops as opposed to on House's mainframe