Well they might have not put it back on if there was damage on the inside of the tire. It's not the blowout when it's on the car, its more that they are worried it may be unsafe to air up. They take safety of employees very seriously and some damage to tires is so bad that it can not be re-mounted. Sometimes unfortunately this is something we are unable to see until it is taken apart.
They probably offered to loan you a tire for their troubles, at least to help you out since you had no tire to mount on the wheel to get your vehicle to Sears, even though we don't want to see you use the competition, it is understandable that you had a warranty there.
I'm sorry they didn't give you the original tire back at first...that sucks...but if you go back they should be more than happy to grab it for you...there is no use in them keeping it. Sounds like they were just trying to help but accidentally forgot to give you back the old tire...mistakes happen, and I hope they apologized and you got your tire back. They just want you to leave happy :)