That's the thing, it's not a likely situation, it's a precautionary measure because it can cause complications later given the way almost every MMO handles a guild type system internally (which is why you can't have duplicate names on the same server.)

You're basically flagged as being a part of x guild, so if your server merges with another and both guilds exists, how would they differentiate the guilds? Especially with the server flag taken out of the equation?