We've done this every version update and will continue to. The extra 10 seconds you might spend realizing your mistake of wrong client is not worth the tons of other players who just won't even be able to connect to emc without information. Plus its not like were turning on a switch. The Bungee Software just allows both protocols to connect, and simply not updating is not always an option (A recent major security vulnerability was released forcing everyone to update bungee -so its not like we even had much of a choice) And the MOTD I do not believe gets the client version.
There is a hacky plugin that does it. I'm not comfortable with it on EMC. We've done it in the past through server changes, not hacking by plugins.
BungeeCord's awesome, isn't it? I've had a great time with bungee cord, and had 1.7 and 1.8 collaborate