When not in the presence of Davis and his cabinet, he wrote Davis very courteous letters and dispatches explaining with great deference that he would not be doing or was unable to do what Davis asked of him.
Lee also routinely made bold moves knowing that his initiatives would already be faits accompli by the time Richmond was apprised of them.
Lee was never, ever ill-mannered in doing these things - but he was not exactly obedient. At all, really.
I would also point out that what Lee wrote in his official orders to his troops and what Lee allowed to actually happen are two different things.
If you break into a Pennsylvania farmer's homestead and take all his stores, all his clothes, all his whisky and eat all his cattle and leave him an I.O.U. payable only in Confederate dollars at drastically below market prices - you're still basically doing the exact same thing as Union troops were doing in Virginia but adding some self-serving paperwork to the mix.
On June 27th, 1863 the "atrocities of our enemies" which Lee was decrying were basically the exact same things his troops were doing to Pennsylvanians at the very time he was writing.
Lee's General Order was basically a document wiping his hands clean of anything that might happen subsequently so it could be characterized as a violation of his orders.
Make no mistake: Lee was in Pennsylvania to resupply his army with clothing, shoes, meat, grain, drink, medicine, tools, horses, mules, wagons, various dry goods, harnesses, etc.
All of these supplies were obtained by seizure from the private citizens and business owners of Pennsylvania.
The Confederate army also made sure to burn down and destroy the home and the business properties of Thaddeus Stevens when they were in Pennsylvania - I believe that was done two or three days after that General Order.
In other words, Lee was not necessarily averse to terror. But he was wise enough to know that terror - as a strategy - could never win the war. He had fought enough Union soldiers and rode through enough Union towns as an invader to realize that the people of the Union would not bow to terror as a method.
Hmmmmmm....
Compare and contrast: Lee's army in southern Pennsylvania in 1863, versus Washington's army at Valley Forge, Pennsylvania in 1776.
Both armies were near starving (well, Washington's was actually starving), and short on every other necessity.
Washington's troops were starving through a winter.
By the time Lee's reached PA, it was summer and they were in pretty fit condition.
Both armies could only pay for supplies with pretty worthless currency -- for Washington, it was Continentals, for Lee Confederates.
So, the question is, did Washington's army treat the local Pennsylvania farmers any differently, or better than, Lee's army?
Somehow, I think a reason Washington's troops were truly starving was that he refused to allow them to plunder the countryside for supplies.
Instead, Washington depended on commissary agents to freely purchase and ship him supplies.
When those failed to arrive, Washington's troops suffered.
Finally, do we know for certain that NORTHERN troops in Virginia took supplies from farmers without ever "paying" for them?