A couple of years ago, I had the same experience where the lower level was more expensive than the general reservations. I'm not in a wheel chair either, but have a bad knee and bad lungs, making going up stairs very hard one or two times, but impossible after that.
I wrote a letter to Amtrak and complained about the higher price for lower level, but did not receive a reply. I, too, feel they are discriminating against the handicapped.
Also, I feel that at least some of the lower level seats should be set aside for handicapped passengers, with or without wheelchairs.
I don't know why a person who is capable of going up the stairs with no problem would want to sit on the lower level anyhow. The view isn't as good for one thing. Another thing is the handicaps often involve personal issues and, as any train attendant can tell you, the lower level area sometimes has a far less-than-pleasant aroma.
If I had any choice in the matter, I'd chose the upper level.