When properties have high non-refundable pet fees like this they are really just saying"we would rather not have your pet staying with us"which is just fine IMO.
There are pet friendly chains(starwood-motel 6)and certain properties within other chains that are not so harsh on pet owners.Stay with one of them,or pay the fee at the other.or board the pet.
BTW-just as an aside.I have found a fantastic product for getting rid of pet urine(feline and canine as well as bunnies and humans)That also tells the pet NOT to do it their again.Private me for more info.