If it were me, I would call and schedule a time to meet with the store manager. Explain to him/her about the file count and the hot pixel then flat out ask for a replacement. In many cases being courteous but firm and direct will get you what you want. You just have to be sure to not make them defensive about the situation, so it is not a good idea to threaten them with reports to corporate, the BBB, etc. Save that tactic as a last resort to use after you have already given them a couple opportunities to make it right.
As for dealing with Canon directly, I have heard conflicting stories. Some say that it will be taken care of. Others say that they claim a certain percentage of hot/dead pixels is normal and would not be covered under warranty. It never hurts to ask them though if you get nowhere with the store.