I use IRC over SSL to avoid leaking my credentials (e.g. NickServ password). You can certainly assume that at least one person in a given channel is logging or on a compromised connection, but that's not the whole point.
- User visits IRC network website
- User logs in
- User is given a single-use token or command containing a token
- User sends token to NickServ
- User is authenticated
Not invincible to MITM, but at least it avoids leaking credentials in plaintext.
Using any sort of authentication involving a separate channel would stop them from authenticating without user interaction. Unless of course it could also be automated. However, I doubt it is easy enough to create a standard for this.
If your only goal is to stop leaking the password in cleartext, that could also be achieved using established standards such as SASL or a challenge-response mechanism such as CRAM-MD5.