Remove Storage iOS Apps on Mac
Quit iTunes.  Then you can go into your "~/Music/iTunes/Mobile\ Applications/" directory, and manually delete apps using the Terminal or Finder.  Before the next Sync, in iTunes control-click to hit the "Reset Warnings" menu item for your device.  During the next Sync, iTunes may ask if you want to (re)copy purchased files from the device.  Just say no.  iTunes will be confused, but the apps will remain on the device, and not on your HD.

It would be better to first make a backup copy of your Mobile Applications directory with Time Machine, or to another HD, before messing with iTunes internal data like this.