Hey, well I'm going to be perfectly honest with you... The wiring on the install from what I can see looks like very good work. Where are the burned wires??? The first thing I noticed was the crimped on ground wire for the starter/alarm. That is a good thing. The other thing I noticed is the tape wrapped around all of the wires. Not many installers do that(the tape helps protect the wiring). Also, the use of wire ties.
This is my honest oppinion... This looks like a dealership that used this as an excuse to not honor your warranty. When I installed my DEI alarm/starter on my X I don't remember having to tap into any of the wires on the SCM... I have NEVER seen an alarm cause computer damage this long after the install (I have been installing alarms for about 10 years), only during install.
I don't know what you can do now, you may still have a shot at getting circuit city to reemburse you. But I guarantee they are going to look at it not seeing any burned wires and wonder why it took almost a year to "Short" the computer system. once an alarm is installed all it does is send the same signals over and over again. If it is working after the install and it was working when the car wouldn't start I would say in my professional oppinion, it definately was not the alarm that caused the problem.