No, you'll still have to keep them in your iTunes. Technically, you can delete them but when you try to sync, the system will recognize 'new purchases' on your device and ask you if you want to transfer them back to your computer. If you choose not to transfer those apps, then your device will sync ONLY with what's in your iTunes.
The backup that resides in iCloud is just so that if you have to restore, everything (including your apps) will look as it did from in your most recent backup. The apps themselves aren't stored in iCloud. It just remembers which apps you had how you had them arranged on your phone and they will download again from (presumably) the Appstore. I just exchanged my new 4S earlier this week and when I restored, all my apps were on phone but wouldn't download until I was connected to WiFi.