Note the Article: One. Article I deals with Congress, not the executive. The scandal is not that habeas corpus was suspended--clearly, Congress has the right to do so--the scandal is that Lincoln, without the approval of Congress, suspended habeas corpus and then ignored a ruling from the Chief Justice that his actions were unconstitutional.
Congress was not in session at the time, and would not be for another eight months, so obviously it fell to the President to take action. Congress affirmed his action as soon as it returned to Washington.
Oh really? Take a look at Section 10, chock full of actions forbidden to the states. Take a look at Section 8, which starts out specifically stating "Congress shall have the power to..." Section 9 does not start out with that statement. Some clauses refer to Congress, others do not. So making a blanket statement that Article I deals with Congress is incorrect.
The Constitution only says when habeas corpus may be suspended. It does not specifically state who may suspend it - Congress or the President. A case can be made for both, and absent any ruling on the matter by the Supreme Court then the final question of the legality of Lincoln's actions remains unanswered.
The scandal is not that habeas corpus was suspended--clearly, Congress has the right to do so--the scandal is that Lincoln, without the approval of Congress, suspended habeas corpus and then ignored a ruling from the Chief Justice that his actions were unconstitutional.
The Chief Justice alone does not have the authority to rule what is Constitutional and what is not. Only the entire court can do that, and so far they haven't done so.