Just to update, I came back from going out of town for thanksgiving to a Fedex package on my desk at work.
I was pleased to find my 5D! Not only had the they replaced the entire mirror assembly, but they had graciously thrown in a new focus screen to boot! Funnily enough, in the "reason for repair/symptoms" field on the printout, they had noted "improper user service". The viewfinder was cleaned to perfection, the sensor looks flawless and of course the mirror assembly and matte focus screen are like new.
I understand that the mirror falls under Canon's recall/replacement extended warranty service, but I am still very pleased that they were kind enough to replace everything! Just another reason why I love Canon, and I'm very excited to put the body to good use in the coming weeks!

