Complex sentence: Lee was disappointed at the state's resistance, a condition that he had not anticipated as many of the fiercely pro-Southern Marylanders had already traveled south at the beginning of the war to join the Confederate Army in Virginia.
Split into simpler sentences: Lee was disappointed at the state's resistance, a condition that he had not anticipated. Furthermore, many of the fiercely pro-Southern Marylanders had already traveled south at the beginning of the war to join the Confederate Army in Virginia.