Comment Re:Complete access to the internal memory? (Score 1) 238
No, it doesn't. You get access to
So the obvious answer is that, if you want security, don't root your phone. It should be kinda obvious that if you can do what you want with the phone via USB, so can any application running on your PC.
You don't have to have USB debugging (a.k.a. ADB) enabled at all. Simply leaving it disables mitigates that concern.
Mounting the phone as a USB mass storage device also doesn't allow you to access the application data unless they store it on the shared SD card storage.