Yes, it came in the box made for the kit - it's so labeled, and there's a photo of the lens on the box and a compartment for the lens inside (it looks the same as the box my 5DII kit came in when I bought it - with lens, that time - early last year, aside of course for the precise model details). The boxes for camera body only are much smaller.
I guess that explains why they are able to sell it this cheap...cuz they are selling the lens separately. Now, did you check your camera and see if it's from the old or new production. My concern is if these are 'flawed' with light leaks or anyother issues Canon provided firmware updates on.
I've not noticed any flaws. It came with the latest firmware installed.