Steve,

The phrase "summary punishment" and "summary judgement" and its obvious permutations never appears in a searchable version of the "Regulations for the Army of the Confederate States," (1863) which is a direct plagerism of the U.S. federal military regulation (just substituting C.S. for U.S.) I suspect your interpretation of an offical sounding (if empty) threat is correct. Military justice was pretty harsh during the period, but still was entirely based on some (often abbreviated) form of due process.