It can be very nasty.....
Depends on the model of alarm and the way it's fitted. I had one on my Blade that took 30 minutes to remove - my mate's R1 took about four hours as it is patched into the wiring loom in about 10 places and we had to work out how to repair the damage.....
Work through it methodically. Take your time and work thorough each wire that has been affected by the installation. There should be no spare ends or breaks in the Honda loom when you're done! It's important to remove every trace of the alarm wiring.
Scotch locked wires are easy to disconnect (there'll be a small plastic connector clipped over the wiring loom wire with the alarm wire coming off it). Some wires may need soldering back together - although my Blade was sold with the wires twisted together then taped over, then taped back into the loom. Make sure you cover any bare sections with electrical tape - if you use black you can pretty much disguise the fact there was ever an alarm on it.
If you need any help mate, let me know! (i'm in Stockport)