First of all its *shouldn't HAVE gotten arrested*As an independent contractor and being self employed, we are not obligated to take the contract if we choose not to. His car, his office, his work space. He shouldn't of gotten arrested. Me personally, I have taken blind people with service dogs at no problem and will continue to.
Secondly, you are incorrect. It doesn't matter if you are an independent contractor you still need to accept service animals, otherwise it's discrimination. It would be the same thing as if you owned a store and didn't allow service animals.
That being said, if you were allergic to dogs, it would be a different story