I suspect that on separation of powers in general we agree. However, consider though what Lincoln and his administration were doing. From the Congressional Globe, July 16, 1861, page 150 and 151, Representative Burnett of Kentucky speaking:
I state, as a member of this House, that the President has violated the Constitution of the United States by his proclamations of the 19th and 27th of April last, declaring a blockade of southern ports. It is one of the incidents of the war-making power to declare a blockade. It is an act of war, and Congress alone has the power to declare war. ...
Men are now arrested in Maryland, and they have been in other portions of the country, upon warrants issued by the Secretary of State alone, and confined in the jail of the District of Columbia. They have not been able to be reached by a writ of habeas corpus; and after they have been kept there for weeks, they have been dismissed without a statement of the charge against them.
The President has also violated that clause of the Constitution which says that no money shall be drawn from the Treasury of the United States, except in consequence of appropriations by law. He has taken appropriations made by Congress for one purpose and applied them to another, in violation of law ...
Article one, section nine, clause five [sic, actually clause six], of the Constitution, declares that no preference shall be given to the ports of one State, over those of another; yet the President of the United States, of his own motion, and without authority of law, shuts up ports still claimed to be within the Union, according to the theory of the Republican party and of the President himself.
As this proclamation was made by the President with full knowledge that the Congress of the United States had, at its last session, expressly refused to pass a bill conferring upon him the power to blockade southern ports and collect the revenue outside of the ports. This blockade has been extended to our interior commerce and trade; and today, sir, the ports of loyal States are closed. My own State furnishes a striking example. Her ports are to-day closed; and her principle railroad virtually under the control and management of the Federal Government. The Constitution confers upon Congress alone the "power to regulate commerce among the several States. " ...
By his proclamation of the 3rd of May, calling into the service of the United States forty-two thousand volunteers for three and five years, by his increase of the regular Army twenty two thousand seven hundred and fourteen men, and adding to the Navy eighteen thousand seamen, he not only violated the plain letter of the Constitution in article one, eighth section, and twelfth clause [actually 12th and 13th clauses], but usurped the powers of the legislative department of this Government.
From Senator Breckenridge the same day:
It is proposed, sir, to approve and make valid the act of the President in enlisting men for three and five years. I ask you by what authority of the Constitution or law has he done this act? The power is not conferred in the Constitution; it has not been granted by law. It is therefore an unconstitutional and illegal act of executive power.
Lincoln could have convened Congress and allowed them to have their constitutional say in what was going on. But no, he waited until July 4. By contrast, Jefferson Davis convened his Congress in less than two weeks once Lincoln called up 75,000 troops.
Question: The power of declaring war resides, according to the Constitution, in Congress. Yet Lincoln essentially declared war by ordering the blockade of Southern ports. How did the Supreme Court react to that? Did that start us on the road to the "imperial presidency," which Congress finally tried to stop with the War Powers Resolution in the post-Vietnam era?
Farber: Lincoln's actions were actually fairly easy to justify under the Constitution. When the Constitution was being framed, the drafters deliberately gave Congress the power to declare war (rather than to "make" war). They wanted the president to be able to act on his own if the country was attacked. In Lincoln's case, a third of the country was in hostile hands, and a U.S. fort had been attacked and taken by hostile troops. Rather than acting like an imperial president, he then turned to Congress for approval. Ironically, his actions came closer to complying with the standards of the War Powers Resolution, over a century before it was passed, than most presidents have done in the modern era.
http://www.press.uchicago.edu/Misc/Chicago/237931in.html