Let us by crystal clear. The SCOTUS ruling in 1842 only confirmed that the SECWAR could act as a conduit for POTUS. The ruling was:
"The Secretary at War is the regular constitutional organ of the President for the administration of the military establishment of the nation, and rules and orders publicly promulgated through him must be received as the acts of the executive, and as such are binding upon all within the sphere of his legal and constitutional authority."
In other words, if the SECWAR communicates an order from the President, it must be taken as if the President himself gave it directly. That is, it confirms that orders prefaced "By order of the President" being promulgated from the War Department have the same legal power is if directly communicated by the President.
No-one has disputed this.
All well, and good, but that also means you should absolutely not be disputing the acts displayed here either. Since, as has been stated, Stanton was acting by order of the president.
What is disputed is whether the SECWAR can issue an order in their own right, rather than promulgating orders from POTUS, and whether the President can invest his powers in a functionary of the state and create a "political commissar" over the army. The answer here is obviously, no. The President is the President, and no-one else is.
Ah I'm so glad we've agreed on this too. But, for the sake of your "Obviously no" answer, let's just unpack this. Word to the wise, I'm just repeating the already existing opinions of Constitutional minds far greater than mine, so, if you do have a rebuttal, I'd ask for some source to back it up as, while your opinion is noted, it is not greater than the already existing opinions of then contemporary legal scholars.
So for whether the president can delegate his powers, let's just look at the phrasing creating the Secretary of War[1]:
"The Secretary of War shall perform such duties as shall,
from time to time be enjoined on or entrusted to him by the President relative to military commissions, the military forces, the warlike stores of the United States; or to other matters respecting military affairs; and
he shall conduct the business of the department in such a manner as the President shall direct."
I'm confused then, what in here you claim limits Lincoln's ability to entrust to the Secretary of War the powers I have suggested which is within Stanton's remit as outlined above?
But let us then consider Cushing's legal opinion of 1855 again:
"I conclude, therefore, on the authority of judicial decisions, and of the arguments, constitutional and statutory, herein adduced, that, as a general rule,
the direction of the President is to be presumed in all instructions and orders issuing from the competent Department, and that official instructions,
issued by the Heads of the several Executive Departments, civil or military, within their respective jurisdictions, are valid ,and lawful, without containing express reference to the direction of the President."
So once again we have a legal mind harking back to the 1842 Supreme Court ruling, which you have already acknowledged is correct.
In other words, McClellan may under no circumstance refuse the dismissal given him by Stanton. He must, legally, assume this directive comes with the blessing of the President. Seeing then that, it is established by law, the president may delegate to Stanton duties relative to military commissions, the military forces and other matters respecting military affairs, then there is no legal leg to stand on for the suggestion that Stanton may not, as Secretary of War, issue orders as he is permitted by Lincoln.
The only limit therefore on Stanton's actions are what he is given permission to do by the President. As is already noted, only Lincoln has the power to veto this decision, and Stanton will have to account for it. However, as established Lincoln may delegate the power to Stanton as he sees fit.
It is then, complete nonsense, to assume that any follow up order, letter or directive, must be issued by the President himself when he may legally delegate the control these matters to Stanton as he sees fit. Like I have stated, McClellan may only request that the order be clarified by the President after the fact, but he cannot, under any circumstance, ignore or defy it. There is no legal impasse, only compliance or mutiny.
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1] This should be noted as not the original 1785 statue for the Secretary of War, but as the later revised statues after the War and Naval Departments had been separated.