Splitting the clip is the way to go. You'll learn quickly that you don't want to waste time processing anything you are not going to use. For example I taught a class a year ago where one of the student rotoscoped 40 seconds of a shot. It took him more than 3 hours to carefully cut out the entire actor when he only needed about 30 frames of the left side of the actors body to pull off the effect.
John, i've been in the same boat a few times. It is a good feature request. By the way, i'm a newbie from FCP and Motion and i'm BLOWN AWAY by the speed and quality of the warp stabilizer here! I just tried a sample with "No Motion". It looks like it was shot on a tripod! Good job, Adobe family!