I think it would probably make sense for mIRC to hide ISO channels in /list. It may even make sense to /part an auto-joined ISO channel and automatically /join the UTF-8 version. That would migrate many users to UTF-8 automatically.
What? mIRC is not the one and only client, we have many users that uses other os' and other clients. Migrating an existing channel to utf8 means that all users have to do it. All webbased clients have to be updated, all java-clients. That's not easy for a normal user without experience in that.
I'd like a workaround like this. It's only an idea, maybe it could work:
if mIRC detects a source or destination that contains iso-characters this channel (or nickname maybe) must be enclosed with a special character that survives the translation to utf8 and back. Let it be ctrl-i (#29) for example.
Then you have only to change the part that receives the input and the part that send it to the server. Using ctrl-i had a nice side effect: it was displayed italic so the user could differ from utf8-names.