Poly bushing's will improve handling, traction and help reduce wheel hop. The only downside is some overall ride comfort may be lost.... But it's a Mustang! Who Care's about ride quality... it's not that bad anyhow. The rear of the car will just be a bit stiffer. Yes they are a bit of a pain to remove but nothing a drill and heat won't solve. As for poly bushings wrecking torque boxes, I have never heard that before, I cant see them doing much damage just because they are a bit stiffer.
Overall if it's a 100% Stock Mustang with no chances of being Moded (Ya Right) and you really do care about comfort stick with the rubber bushing's. It's a matter of preference. For improved handling and all that other good stuff I mentioned above go with the poly's. Now that I look at your sig (I Just Looked) I'd definetly go with the poly bushing's. Infact I would consider getting a set of aftermarket upper's and lower's as they offer a big improvement over stock one's and are alot stronger. (Aftermarket Cntrl. Arms Usually come with poly bushings as well) Chances are your car is going to see more mod's in the future and as power increases so does the need for traction and stronger suspension components, and you will definetly need some good control arm's as the factory one's just wont do the job.