My county health department has told me that only a "guide dog in harness" has to be admitted to my restaurant. If I follow their advice, am I violating the ADA?

Yes.  Any service animal and their owner must be allowed to access those areas of a restaurant where customers are allowed to go.  Whenever a public health ordinance, or other local law, is different from the ADA, the law which is least restrictive for the person with a disability takes priority.  

For additional information, take a look at the following resources:

FAQ: What if a service animal barks or growls at other people, or otherwise acts out of control?

Service Animal Resource Hub

Service Animal Misconceptions