I would like to have a shield permanently attached that use the VIN (not 5v) for it's power - the problem comes in when I want to program the arduino (via the USB port), do I need to also have the barrel connector plugged in, or can I just expect the shield to not work (no, it won't be damaged from not getting enough/any power), but have the arduino itself be fine - or am I somehow damaging the power regulator by attempting to use it in reverse?
You do run the risk of damaging the 5V regulator, yes.
Power will attempt to flow from the 5V rail (USB port) through the voltage regulator (backwards) and into the shield to power it.
As your shield doesn't mind being under-powered from 5V while you're programming the Arduino you can add a diode between 5V (anode) and Vin (cathode). This will bypass the regulator when the voltage of the 5V rail is higher than the Vin rail, and your shield will be supplied with about 4.3V (slightly higher for a schottky diode).