But it is a requirement that they not discriminate against customers with disabilities. Charging an "exorbitant fee" for a driver who would tolerate a service animal would be a form of discrimination, even if that fee was the organic result of a pricing algorithm.
The law sets a high standard that we should all strive to meet but the courts tend to be full plaintiffs who have been wronged by companies failing to provide even the bare-minimum service. This appears to be the case here and we should probably focus on how to grasp the low hanging fruit before trying to come up with the "perfect" solution.
Yeah in this case, a driver may have to take a service dog even if they have fear or an allergy, or Uber could be sued again. IANAL, but this is my understanding.
There's more interesting arguments to be made, like you can't ask the driver to provide proof of their allergies, and so on.
The rules are pretty clear that an allergy isn't a good enough reason to deny service, but it says that Uber should try and accommodate employees that don't want to be around dogs for whatever reason: https://www.ada.gov/service_animals_2010.htm
You need to read the rules more carefully: they mean Uber, in as much as it is in control of the rideshare service, can't deny people on that basis. The individual drivers can and their employer must accommodate them under the ADA.
If the drivers aren't employees and are self employed then as they are a business of less than 15 employees they can refuse anyone they want for any reason.
So in your example, the business should have a different waiter/waitress provide service.