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.
You cannot be serious. This issue has been before the Supreme Court at least twice (Ex Parte Bollman and Hamdi v. Rumsfeld), and this very issue—Lincoln’s suspension of the writ—was before the Chief Justice when he rode circuit. In fact, it was so well-settled, that Taney even remarked surprise when the case came before him:
“And I certainly listened to [the President’s argument that he could suspend the writ] with some surprise, for I had supposed it to be one of those points of constitutional law upon which there is no difference of opinion, and that it was admitted on all hands that the privilege of the writ could not be suspended except by act of Congress.”
In Taney’s opinion in Ex Parte Merryman, here’s his response to your statement about Article I:
“The clause in the Constitution which authorizes the suspension of the privilege of the writ of habeas corpus is in the ninth section of the first article.
“This article is devoted to the Legislative Department of the United States, and has not the slightest reference to the Executive Department. It begins by providing “that all legislative powers therein granted shall be vested in a Congress of the United States, which shall consist of a Senate and House of Representatives.” And after prescribing the manner in which these two branches of the legislative department shall be chosen, it proceeds to enumerate specifically the legislative powers which it thereby grants, and legislative powers which it expressly prohibits, and, at the conclusion of this specification, a clause is inserted giving Congress ‘the power to make all laws which may be necessary and proper for carrying into execution the foregoing powers, and all other powers vested by this Constitution in the Government of the United States or in any department or office thereof.’...
“It is the second article of the Constitution that provides for the organization of the Executive Department, and enumerates the powers conferred on it, and prescribes its duties. And if the high power over the liberty of the citizens now claimed was intended to be conferred on the President, it would undoubtedly be found in plain words in this article. But there is not a word in it that can furnish the slightest ground to justify the exercise of the power.”
Besides Taney’s opinion, this issue was also before the Marshall court in Ex Parte Bollman, in which Marshall stated, very clearly that “If at any time the public safety should require the suspension of the powers vested by this act in the courts of the United States, it is for the legislature to say so.”