Lee was certainly concerned with how his army acted in Maryland in the interest of gaining support from that state. The state was fairly well divided, and, if I recall correctly, most of the pro-Confederate population was further east and south. In the Frederick area, I believe there was a stronger Unionist sentiment.

While David quoted Jefferson Davis' perception of Lee's campaign, Lee's own letter to the citizens of Maryland took a much more empathetic approach, even claiming to be marching into their state to help them:

"Believing that the people of Maryland possessed a spirit too lofty to submit to such a government, the people of the South have long wished to aid you in throwing off this foreign yoke, to enable you once again to enjoy the inalienable rights of freemen, and restore independence and sovereignty to your State. In obedience to this wish, our army has come among you, and is prepared to assist you with the power of its arms in regaining the rights of which you have been despoiled." -- R. E. Lee to "The People of Maryland," Sept. 8, 1862 (O. R., Series 1, Vol. 19, Part 2, 602)

From this letter, Lee certainly did not seem to consider the people of Maryland enemies, but the victims of a common enemy. He portrayed his campaign as a liberation.