I would guess that the cost of those towel animals going to "new homes" has already been calculated by Disney and is in their marketing plan. I am sure we all paid for those towels. I have never taken any, but I will be taking any home that I receive on our next trip. If Mousekeeping says yes, the manager at the front desk say yes, then I say "yee ha"!
I guess it goes right along with using the coffee they supply in the room, you don't get a credit if you don't use it, or the shampoo etc they supply. Some things are including in the cost of the room, I bet the towel animals are included in that cost as well. If people stopped taking them home, I would be willing to bet we wouldn't see a discount in the room prices because mousekeeping isn't creating/washing/buying towel animals.
I say, congrats to anyone who receives the "gift" of a towel animal !