[BroJoeK]

rusty: "One that has always struck me as particularly onerous was the arrest of elected officials of a state legislature for action that they might take in the future.
Were they guilty of a thought "crime"? Where does the Constitution allow arrests for thought "crimes" or the possible future "crime" of doing what authors of the Federalist papers agreed the Constitution allowed them to do?"

Doubtless, you refer to Maryland.

1. First, please describe how the Union's treatment of Confederate supporting Marylanders was different or worse than the Confederacy's treatment of Union supporters in such places as East Tennessee?

2. Second, note that Maryland's legislature voted 53-13 against secession, on April 29, 1861.
   This was still a week before the Confederacy formally declared war on the United States, thus constitutionally turning Copperhead Northerners into traitors who met the criteria of:
   Article 3 section 3: "Treason against the United States, shall consist only in levying War against them, or in adhering to their Enemies, giving them Aid and Comfort."

3. Once the Confederacy formally declared war, on May 6, 1861, then the Union army did what was necessary to suppress treason in Maryland.

rusty: "The sentence was set aside by Lincoln who imposed exile.
Where does the Constitution give Lincoln the power to exile people?"

Of course I agree that exiling a copperhead Ohio congressman to the Confederacy was the most cruel, inhumane and doubtless unconstitutional punishment imaginable. ;-)
As for the legalities, I'd suppose that since the worthy congressman was tried in a military court, then the Commander in Chief has some authority to modify or commute its sentences:

Article 2, section 1: "The President shall be Commander in Chief of the Army and Navy of the United States... and he shall have Power to Grant Reprieves and Pardons for Offenses against the United States..."

rusty: "During the war, the South had a court system that did help protect civilians against the military."

And you can cite examples of this in Union sympathizing areas of, for example, East Tennessee?

[rustbucket]

As for the legalities, I'd suppose that since the worthy congressman was tried in a military court, then the Commander in Chief has some authority to modify or commute its sentences:

I recognize that as head of the military Lincoln had the power to reprieve or pardon the sentence of a military court, even one that was unconstitutionally trying a citizen when the civil courts were open in a state that was not in insurrection. But exile? Throw someone out of the country for exercising his first amendment rights?

Take a look at the trial transcript sometime. Vallandigham recommended in the speech for which he was arrested that people use the ballot box to remove Lincoln from office. How unpatriotic! Treason! Can't have that, can we? IIRC, Vallandigham did also call him "King" Lincoln. Well, a king does have the dictatorial power to exile someone from his country, so I guess Vallandigham was right.

As the Indiana governor's letter to Lincoln said in part about the Vallandigham arrest and trial (here is the link again: Governor to King):

According to my views of the question arrest, imprisonment and trial, under Gen. Burnsides' Order, No. 38.1 are a clear violation of the Act of Congress, approved March 3rd 1863, providing for the suspension of the Writ of Habeas Corpus and regulating arrests in States, in which the Administration of the laws, has continued unimpaired in the Federal Courts.

If the General Commanding the Department, can issue his orders establishing a new class of offenses and arrest, and try persons for their violation by a Military Commission, then the Act of Congress amounts to nothing.

But aside from this, I am satisfied that the effect of the order is bad, and that it has wholly failed to accomplish the purpose for which it was intended; that on the contrary it is greatly intensifying the hatred of the masses of the Democratic party, toward the Government, and is rapidly converting what in many, was mere clamor and general opposition to the Administration into bitter hostility to the Government and the War.

...

My judgment is against all this business, as illegal and highly inexpedient ...

Couldn't have said it better myself.