This might sound a bit stupid, so forgive me for that, but I'm really curious. I understand that if you were to change servers that you would be ineligible from obtaining [Realm First!]-achievements for 2 months, but what about when you switch from Horde to Alliance on the same server? Do the rules still apply?
Unless you're talking about Personal Realm First for 5.2 (of which I'm unaware of any) there is no cooldown or preventative measures from a guild getting realm firsts for raiding regardless of faction change, realm change etc.
Gamble on Mal'ganis xferred from Zul'jin and received the Realm First Achievements for Heroic First Kills.