not bury it in a jewish cemetery? Why have the taxpayers bare the cost?

This isn't about taxpayers baring the cost. This was about permission from the state's environmental agency. NY State does not allow anyone to put a large amount of stuff in the ground without proper vetting of what that is and whether it is a danger to the environment. They were just checking it. The state was treating the religious organization as if it is just another organization and held it to the same rules. If anything it is proof of the separation of church and state.