Other articles have been saying not to be alarmed because if the committee deadlocks, the automatic defense cuts won't come until 2013 and can be reversed by the next Congress. That is cold comfort, but it still focuses on the revenue actions of the committee. This article raises the specter that other permanent legislative matters could be run through the same protected committee process and fast tracked into law.
Of course, another problem with this committee is that if the committee even attempts to raise revenue/taxes then it will violate Article I Sec. 7 of the US Constitution which explicitly states that only the House has the right to initiate revenue bills. This power does not lie in a Joint Committee, it belongs solely to the House of Representatives. Of course, the House will pass the back along so they don't actually have to take the blame of raising taxes...they'll just blame the committee. Then the powers of the House will gradually be lost to the committee who will become real legislature. If the House won't even defend its own constitutional authority from usurpation, then our system of checks and balances isn't working as intended and the Constitution itself is in danger.
The points you raise about the Super-Committee being abused to circumvent the normal process of republican government in order to force unpopular legislation through Congress is a great threat to the Republic as well. This Super-Committee seems somewhat reminiscent of the old Politburo of the Central Committee of the Soviet Union.