The AF screwdriver on Nikon AF bodies is spring loaded. If you mount a manual focus lens, the lens flange pushes the screwdriver back into the body, whether the body is set to manual or autofocus. No damage to either lens or body should occur.
The MF/AF switch on the body (which usually says M/S/C), retracts the screwdriver to disengage the AF drive from an autofocus lens.
My guess is that on your body/lens that wouldn't autofocus, either the screwdriver or the lens slot that receives it was slightly out of alignment and they weren't engaging. If this happens you can try examining the driver and slot to see if anything is out of alignment, and gently poking the driver and slot to make sure they are moving freely and in the proper position - the slot should be only a tiny bit recessed from the lens mount flange.