Hmm. Something doesn't yet match because if you export Full Quality from iMovie, the output will have .dv suffix...
Anyway, you do save time and harddisk space by using iMovie's tiny reference movie as an input: Quit iMovie and open JES Deinterlacer. Open its Input tab, press "Choose...", navigate to the iMovie_project/Cache/Timeline Movie.mov and select it as an input.
Notice that JES Deinterlacer may stall if it is hidden (via Hide Others command, for example) so avoid doing that when it is active. If JES Deinterlacer acts up, you may need to quit JES Deinterlacer and delete its preference and log files (~/Library/Preferences/JES Deinterlacer Prefs and nl.jes.deinterlacer.plist and ~/Library/Logs/JES Deinterlacer log). Then log out/in and try again.
http://www.sjoki.uta.fi/~shmhav/SVCDon_aMacintosh.html#interlacing