The decision not to prosecute treason was political but not made by SCOTUS. It was a decison of theexecutive branch. As to the author’s contention that Chase contradicted himself by declaring that the union of states was declared perpetual by the Articles. He asks how can the Articles declaration be used when they were replaced. But the Articles never claimed to be perpetual. It claimed the Union of States was perpetual. That is what Chase referenced. The adoption of the Constitution did nt abrogate laws passed under its auspices. The Northwest Ordinance remained law of the land and the statehoods of the Old NW were governed bythat law. The passing of the Articles had no bearing on the nature of the perpetual Union.
Mercy. Clemency.
First of all, even if you believe that citizens of Confederate states could not legally commit "treason" against the United States -- since they were then part of a "different country" -- citizens of Union states who gave "aid and comfort" to the Confederacy did meet the Constitution's clear and simple definition of "treason".
And yet, during the entire Civil War period, only three incidents resulted in convictions for treason, and all seven people hanged were civilians:
After the war, a number of Confederate leaders were indicted for treason -- including Jefferson Davis and Robert E. Lee -- but all received blanket amnesty from President Johnson (Democrat from Tennessee) on his leaving office in 1869.
"President Andrew Johnson, in a proclamation dated December 25, 1868 (15 Stat. 711), gave an unconditional pardon to those who "directly or indirectly" rebelled against the United States.
Bottom line -- President Lincoln's peace offer to the Confederacy amounted to: Unconditional Surrender in exchange for no treason trials.