**SOLVED**
I know this is an old thread, but I was looking for the answer to this question as well. Basically, with iCloud I only want to sync my iPhoto library with my iPhone via iTunes...nothing else.
I was racking my brain trying to solve this issue, and I believe I have found the solution.
On the Summary Tab in iTunes, select "Backup to this computer" and then perform a backup. Then go to the apps tab and deselect the Sync Apps check mark. When I did this, iTunes asked me if I wanted to keep my existing apps on my iPhone or delete them. I opted to keep them on my iPhone.
This does not delete your previous iCloud backups. Furthermore, a backup to the computer actually captures all your apps and their data in the event you'd like to restore from the computer backup sometime in the future.
**NOTE** This will turn off iCloud Backup on your device (IT DOES NOT DELETE iCLOUD BACKUPS). Simply finish the iPhone to iTunes sync via the computer. Disconnect your iPhone/iPad. On the iPhone, go to Settings > iCloud, and turn the backup to iCloud feature back on!
Once you've told iTunes not to sync the Apps, you should not have to worry about it anymore. However, any additional changes you make in the future will require the same steps above.
Hope this helps.
Cosmo