I'm wondering why the refinisher didn't stop applying the stain when it was first noticed that the color didn't match? This would have been noticeable with the first swipe of a brush and stain.
If you want the stairs to match the rest of the wood floors then starting over is your only option. Refinishing the hall with the darker stain is an option as long as you like the color and the expense it involves.
I think it would be cheaper to redo the stairs with a matching stain. This way you won't have to refinish all remaining floors to match the dark color.