How to delete an app from device using iTunes?
Why are you trying to do this via iTunes? You should delete the app on the phone and use the app store on the phone to re-download it.

However if you feel you must do this via iTunes after you have deleted the app from the phone, go to:

~/Music/iTunes/Mobile Applications


…and delete the application from there.

You can then download it again via the iTunes store and re-synch the phone.