For all intents and purposes in won't hurt to freeze an animal whole to be processed later. However, if you are going to leave it in the freezer for more than a week or two, you should wrap the animal up in a plastic bag to protect it from freezer burn.
I was once asked to do a skinning demo at a spring trapper's meet. They gave me a coon that had been just laying loose in the freezer since trapping season. This coon was freezer burnt on each leg, all the way to the elbow, and the entire face was freezer burnt. The skin was the same consistency as cardboard, and I could not finish skinning it.
Also remember, if you take these animal out to skin later, you'll need to let them thaw in a "cool" place. It will probably take 24 hours or more to thaw the animals. A big beaver can take two days to thaw.