Yes he could, under the laws in place at the time. But just out of curiosity, what do you suppose the 100,000 confederate troops called up in legislation passed on March 4, 1862 for?
Step away from the bong, sir. You've got the date wrong in your alternate view of history.
Are you serious? It is called protection- the purpose of government. There was a new confederacy which required troops for protection just as any real country does. Only this was more important since the storm clouds of war were gathering in the Lincoln administration. Lee knew only too well what Lincoln was preparing since it was to Lee that Lincoln offered the command of the US Army in 1861.