Secretary of War Stanton (1862-65) was a Democrat originally, but Lincoln appointed him because he was the best man for the job. Lincoln defended Stanton against his critics calling for his replacement stating, "If you will find another secretary of war like him, I will gladly appoint him." Stanton converted to a Rep and was the one who said at Lincoln's death, "Now he belongs to the ages," and lamented, "There lies the most perfect ruler of men the world has ever seen."
Secretary of State Seward (1861-69) directed the arrest of thousands of citizens for sabotage, spying, disruption of the draft, or promoting insurrection. He implemented the suspension of the writ of habeas corpus. I have found no evidence that he expressed any criticism of the President, at least during the war.
I thought it was Stanton, the Secretary of War, but I've pulled an all nighter with the fans of these six ex-generals.