I will post this here so I can link to it.

Code:
/run ChatFrame_AddMessageEventFilter("CHAT_MSG_SYSTEM", function(self, e, msg, ...) if (msg == ERR_CHAT_WRONG_FACTION) then return true; end; return false; end)
this macro will filter out all the "You can only whisper to members of your alliance." messages that you get in BG.
Believe it's caused by addon calling SendAddonMessage() as whisper to a cross faction player.