A few years later one of my agents was in a horrific accident and when he finally got out of the hospital he was confined to a wheel chair and little movement.

Just because someone is not in a wheelchair, doesn't mean he/ she is a fraud.

The lower units are wheel chair accesible. 

For example, alert someone with epilepsy they're about to have a seizure, get between a vet with PTSD and other people if he/she starts to get stressed out, and of course, pick things up off the floor for those in wheelchairs, and seeing-eye dogs, etc.But, companion animals are not allowed to go everywhere with their owner.  

I understand that to be correct ^^- the law treats it like a wheelchair or any other external accommodation that would be illegal to discriminate against. 

However, there are a wide range of TRAINED service animals; some that (for instance) pull wheelchairs or open doors for owners unable to do so.

A reasonable accommodation is something that a person with disability needs that somebody without that disability can do without - so housekeeping assistance might be an example here, sort of like a wheelchair ramp for those confined to a wheelchair. 

You could apply the same matters of running an efficient operation to having to take time out to oversee a ramp being set for wheelchair access, putting in grab bars in a shower or removing lower cabinet doors in making reasonable accommodations.

I have been told that if you wouldn't charge more for someone in a wheelchair, you can't charge more for someone with a service animal. 

Most disability law experts feel that requiring a deposit would be the equivalent of charging an advance damage deposit for someone in a wheelchair.