Muh I didn't know #ally was a function already. We tried to set an alliance but currently alliances are disabled due to WoE decisions.
We will need to get that enabled in order to test if it does work now or not.
EDIT: So we did @channel join #ally and we did confirm that this does work.
The function I was describing would be solely for guild members and allied guilds to talk with each other, so basically keep it between allied guilds and not anyone who joins a channel like #ally.
When you send messages in guild chat, the chat color is green. #ally would technically function the same way for all allied guilds, but if #ally exists as a channel already then there would need to be another way to create what I'm (hopefully) describing.