Does unchecking them and having the "only update checked songs" option ticked work?
Personally, I plugged in my iTrip, set it to the station I wanted then deleted all the iTrip tracks out of my library. Hey presto, my iTrip's on a frequency I want and no iTrip stations appear in any of my (smart)playlists without having to edit any of them. Obviously I can't change the frequency when I'm out and about, but I never want to anyway.
Either of the above may work for you.