Governments are in need of money all over the world, and they will come up with ways to get them (even if it means breaking human rights or constitutions). The little guy (the affiliates in this case) won't fight back - it would take a lot to get people marching in the streets.
The big corporations will fight back though, and that seems to be what we see here, a corporation saying "we prefer to earn nothing, than to let ourselves be subjected to unfair taxation". From the company's POV, this is surely less about this particular instance, and more about a wake up call to other states that are thinking of following suit. The affiliates are innocent victims, but I would still think of them as victims of their own government's policies, not of Amazon. California is changing the rules of the game, and it seems like a fair reason for a company to rethink the opportunity of having anything to do with that state.