bitcoind is the bitcoin protocol. You can't have two different protocols that would be compatible. One thing you're forgetting are the miners. If there were to be a drastic change in the protocol, at least 50% of the miners would have to agree to it, thus I don't see a problem with having one "official" client representing the protocol. For everything else (gui, taint analysis, etc), we already have several clients that follow the same protocol, and you are free to use any one of them.