The problem with removing a nick from the nicklist because you don't want to see it is a mute one imho. Don't look at him. If you /ignore a user, for all reasons and purposes, the user no longer exists to you. I don't see an additional benefit in removing his nick from the list.

That said, the nicklist displays the nicks that are in the channel. To not make it display all of them defeats the entire purpose of having one to begin with.

I also believe (personal opinion !!! ) that if you don't even wanna see a user's nick being the the channel, then
a] apparantly you are the one having issues, not the user in question
b] you don't care if the user is there, but apparantly you care enough about the user to make sure whether he is in the channel or not.

Just stop thinking about the user, don't pay attention to the nicklist.