If you just unplug the wire from the trans, it will throw a code because the computer knows it's not connected. The only way to get around this is to plug in a 2.2K ohm 1/2 watt resistor so the car thinks its still plugged in.
www.ls1.com has a section on doing this mod. I went with the SLP Eliminator, it's like the stock weather pack plug so I don't have to worry about water or other crap getting in there. And yeah, the skip shift light still comes on.