I have the same behavior with my ipod touch.
I found that the Mobile Applications folder under iTunes folder gets bigger with this backups. Actually I have multiple instances of the same application (numbered 1, 2, 3...) even when that application haven't been updated since their first version.
I guess the sync issue is based in the fact that you can't control which application you want to be synched back to your computer. If you delete one app on the computer and also purchased a new app on the ipod, next time you sync then you'll be forced by iTunes to choose between transferring BOTH apps back to your computer, or not transferring the app bought and keep the deleted app (from iTunes) in your iPod (unless you delete it to from your iPod, which means that every time you want to delete an app you must delete it from iTunes and the iPod or iPhone).
I would prefer a little bit more control at the sync time of which application should be synched back to iTunes, or deleted from the iPod (perhaps a simple automatic sync which looks for the last action you did would do the trick) but this depends on Apple engineers 🙂.