They probably got spared due to Salmon Chase being tired from the involvement in the impeachment of Andrew Johnson and the nation was "healing" from the Civil War.
Lee was spared because of Gen. Grant's parole of all the surrendering Confederates (at Appomattox Court House)... when Grant heard about plans to arrest Lee, he threatened to resign from the army, believing it would violate the terms of the surrender agreement. President Johnson backed down.
A very classy move by Gen. Grant.
Of course, Lee was never a traitor anyway, as he was a citizen of the CSA during the war. To open another can of worms.