it seems like [IP addresses is] generally a bad thing to encourage other alternate implementations to create this backdoor that isn't really being used.
Agreed. Not as many users will be as intelligent or aware of such security issues with using IP addresses. It is best to not have that option at all.
I get that backward compatibility with earlier clients might make it useful to keep these messages for a time, but at this point the entire notion of sending transactions to an IP address is almost completely refuted as a really bad idea.
The bitcoin project is entirely open source. The older source code versions are all freely available and backed up. If people want to use ip addresses, they can dig up the old code, and release a forked version for only those people that would want to use ip addresses. But best thing is that ip addresses are not included in any official versions. Security trumps usability and extra options.