I also wanted to remove App Store update's for iMovie, as well as all the iWork apps. Also for me, starting in OSX 10.9, right clicking on an update in the App Store no longer produces the Ignore option. I was able to work around the problem. You will need to download a copy of the new version of iMovie, but you'll delete it once you are done. Prior to downloading the new iMovie, either remane it, or move it somewhere, so that it isn't deleted during the download. Inside the new iMovie application (right click on the application and select Show Package Contents), then inside the folder called Contents, you'll find a folder called _MASReceipt. Copy this folder into the Contents folder of the old iMovie application. You can then delete the new iMovie and rename or replace the original iMovie. Once you do that, the App Store apparently believes that the old version of iMovie is the new version, and will not longer list iMovie as an available update.
I have used this for the iWork applications as well. While I haven't used them extensivly since making this change, they appear to be working normally.
We'll need to do this each time one of the applicaitons is updated, but at least we can get ride of the notices.