The dealership has everything to gain and nothing to lose by blaming the problem on circuit city. If you had nothing in there aftermarket, they would have to pay to fix it. Do you have any more pics? I can't tell by the pics, but I would be willing to bet that circuit city soldiered every connection on the car. Circuit City doesn't use wire nuts or crimp because it isn't as good as soldiering. I think if you look closer to the connections on the alarm you will see that they are soldiered. It will be hard to tell now how it was connected to the car now that it is out, but an installer that goes to the trouble of wrapping tape around every wire, usually doesn't do a hacked up job. The installer that did this wasn't a rookie in my opinion.
The other thing is, in the first pic, you see the black wire with the yellow stripe? That is the starter wire. I don't know at what point this pic was taken, but I hope the dealership soldiered that back and taped it. The Last thing that is concerning to me is that the fuse box is pulled out. The fuse box doesn't have to be taken out to install the alarm. Why did the dealership remove this?

What did you say you had your car in the first time for? Recalled fuel sender? You think it is possible they shorted something out while changing the part for that? This would make more since to me. Not an alarm that had been working for almost a year with no problems. You said yourself that the alarm was working just fine. If it had any problems every fuse that you can see there would be blown and it wouldn't be working. Again, this is just a way for you to pay for it, not them. It so easy for them to blame it on that, and I don't think you can do to much about it.
I hope you don't get irritated at me for my opinion. I don't like circuit city myself, they treated me badly and thats why I don't work there any longer. I CAN tell you the way they work and what I see.