The difficulty is when there is a power asymmetry in the original agreement, as there normally is when it's an individual signing a contract with a larger organization.
Two large companies agreed to arbitration? Stick to the original agreement, as both sides paid lawyers to advise them on what to do, and there was almost certainly a negotiation. But individuals don't, usually, have the resources to hire lawyers or the ability to do the kinds of negotiations required to get favorable contracts. In such situations, I am troubled that we can end up signing away our ability to appeal to the courts to intervene on our behalf.
If this issue gets enough press for a long enough time, I could see legislation that voids arbitration clauses in certain cases.
I can see value, and certainly abuse, in people agreeing to allow their religious organizations to arbitrate civil disputes... it would seem that people should be allowed to make the choice and suffer the consequences if the agreement is within the established law.