At a Microtel Inn & Suites where I stayed, they had a pet fee of $10/day ($5 for longterm stays). They addressed the registered / unregistered problem by posting a large-print sign next to the front desk which said:
Registered Pets: $10 / day
Unregistered Pets: $50 / day
To the OP, I would recommend just finding a place with a lower pet fee.