You can match a warp stabilized shot with with the original to only stabilize a portion of the shot but you need to carefully choose the transition point. You can even cut up the shot and stabilize different parts with different settings. The key to making the cuts invisible is to use scale and/or distort tools to perfectly overlap the frame where the cut is made. This requires an overlap of one frame, so it makes a difference how you cut up your clip.
The key to getting a perfect match on the shot you are scaling to match is to use the difference blend mode. When you have the pixels lined up perfectly you will be able to see it easily.
Other than that, an approach like the one Mylenium suggested is a good place to start.