Pretty much that's what they are going to have to do since the SC has said unless Amazon has a physical presence, they cannot tax them.
Whether or not their Kindle/A9/whatever subsidiaries counts as a physical presence is like you said up to Congress and/or the courts. Right now it's ambiguous and you can't blame Amazon for doing what they're doing.
But that ruling was back in the early 90s and didn't really cover the specifics that California is trying to use in their law. They haven't made a ruling on the subject since. Since nexus is an ambiguous concept and Congress hasn't fleshed it out, states are filling in the gaps and forcing the issue on the courts to reach some sort of clarity.
And again, it isn't a tax on Amazon. They would just be forcing Amazon, which has a physical presence, in a technical sense, to collect the tax the citizens already owe, just like a B&M store in the state would have to do.