How to stop syncing apps with iTunes without wiping them from my iPhone?
What worked for me was to setup my device for wifi sync first. Make sure under the edit menu and preferences / devices (this is important) that you have it set to prevent automatic sync. Right click on the device in the left pane of itunes and reset all warnings. Have the cable disconnected but the device still visible via wifi. Uncheck sync apps, then ok the warning about removing the apps from the device. Then click "summary" and uncheck sync over wifi then apply in the lower right.

Now reconnect via cable turn wifi sync back on and sync your device via wifi or cable doesn't matter which. Now disconnect the cable, goto apps in iTunes and delete all apps. Ok the warning about removing the apps from the device. Goto summary and uncheck sync via wifi and click apply in the lower right. Then you can reconnect with your usb cable and turn on sync via wifi again.

At this point a popup will tell you that there are apps that you need to transfer to iTunes or they will be removed from your device. Check don't show this again and then click don't transfer. Now you can go into edit and preferences under General and uncheck apps altogether if you want the iTunes apps folder to go away as well.

I did this with both my iPhone and iPad2 and I still have my apps on them.

Good Luck.