How to remove apps from iTunes?
Yes - just delete the apps from your Library on iTunes and they won't show in the list of apps that could be synced.



The long version is click on Apps in the Library, then select one or more apps and press the delete key. Answer a few dialog questions to confirm you want to delete and move the file to trash (or not) and you are done. The next sync will remove that app from your iOS devices.

Do note, that if you don't sync for a while, the iTunes could see the apps on the device as new and needing a transfer back to your library, so be sure to sync sooner or just pay attention when a "items were found on your device" dialog pops up and asks you to transfer purchases back to the library.