I'm just getting rid of the fuguly mudflap on my '06 now too and plan to just cut the wires off as close to the connection as possible. You can maybe pull back the rubber piece that covers the connection to see if there's connectors that unplug but my guess is they're soldered at the connection.
There would be another connection at the battery end of the circuit and that may be under the seat. I'm cutting mine at the plate light end so I can re-route the same wiring & re-connect to a new plate light on the fender eliminator which will be installed in a different location. If you don't want or need the plate light then you could maybe disconnect near the battery without cutting anything. (gotta have one here - it's the law).
if you take the tail off and the front seat off you can follow the wire to the connection. you can unplug it there and fish the wire out and take the whole light off. the through some electrical tape over the connector just so no water gets in it or anything. that's what i did to take my rear fender off. then i took the plate bracket off the fender, used an L shaped piece of metal and bolted the plate bracket to that and to one of the screws under the tail light. just for now till the 2bros gets here
Think I'll try that method now instead of cutting at the light connection - makes more sense in case stock part is needed down the road. Would have to do that to re-route the wiring to the F.E. that will be position up under the rear wheel anyway :clap