how do you replace the ignition lock cylinder assembly, the keys will no longer

Not too difficult. Be sure to have a drill, drill bits and a bolt extractor set : http://www.ehow.com/how_7645029_instructions-lock-cylinder-honda-civic.html

New key(s) and immobilizer receiver will need to be programmed , OR , before you put the new switch in , have it re-keyed (locksmith) for the CARS ORIGINAL key , AND swap over the receiver ring from original lock.