That's a valid point, but you won't be effectively encrypt incoming email in the layer of a webmail client. You'd be better off incorporating that before the message is even saved to disk - in the mail delivery of your MTA. So once again it wouldn't be PHP (I hope for your sake!).
"(And in regards to in-browser crypto - I'm unsure there are strong enough guarantees of security in javascript to make me entirely comfortable having my private keys and passphrases hanging around in the process space where rogue javascript and/or plugins might be able to scoop them up…)"
Your sarcasm is entirely valid, but you didn't actually look at the project that you are criticizing. The entire point of what I linked in my comment is that nothing critical should be exposed to the JavaScript, just an API that it can interact with to send commands to: such as keygen, verify this message, send cleartext and receive ciphertext in response, etc. You're preaching to a believer here, :-)
Your ~/.gpg/ is -not- accessible to JavaScript. The interface, the GnuPG binary, is. That's the point. Now we can both agree that exposing private keys in such an API is a bad idea.