Pull it out by tracing each wire. Pull one at a time so you can tell if anything is disconnected. The only thing that may be left disconnected is the yellow starter wire in the ignition harness (if that particular alarm has a kill switch). Then you would just connect the starter wire back together. The only other things it should run to is main power, ignition power, door pin wire, lights, and maybe a siren under the hood.
And you can leave that led in place so you don't have a hole in your dash piece. You can hook it up to something else later down the road if you want. They usually take 5v rather than 12v though.