The only way to argue that Taney's actions in Treasury were contradictory to his later responsibilities as Chief Justice of the Supreme Court is to argue that he somehow violated the Constitution while he was acting as Secretary of the Treasury.  However, there is nothing in his actions at Treasury that did this in any obvious way.

At Treasury, Taney's main action was to remove federal deposits from the Bank of the United States and to deposit them in the "pet banks" in the various states.  This did act to kill the Bank of the United States, which the Supreme Court had ruled Congress had the right to create.  However, the Supreme Court did not say that the Constitution said there had to be a Bank of the United States, just that it said there could be a bank.  Therefore, what Taney did was not contrary to the Constitution.

You could argue that Taney's actions were unwise or that they were bad for the country, but it is very difficult to argue that they were contradictory to his responsibility on the Supreme Court.