This is truly a basic question about guilds, and GuildWiki confirms it, but why is it ANet decided that all characters on an account must be in the same guild?
Mostly because unlike other online games, GW has almost instanteous map travel. Thus, the relationships you form with other players are made with them, not with their characters. Unlike other games where level 40s stick together and form guilds with other level 40s, etc.
If I had to guess, and that's pretty much all you're going to get on this string, I'd say it was related to PvP (or more specifically GvG) as it was in place before PvP characters were introduced.