Lee made a choice. In my opinion, he didn't make the right one. I understand why he went with the CSA, so I wouldn't call him a coward.
We can throw around the idea of Lee being a coward as much as you damn well please, he had reasons for what he did. Maybe he thought he could have gotten the CSA to abolish slavery later on. Maybe he thought that the southern states would come to their senses after a year of war, I dunno.
Still, depending on which way you see it, he was either a man of great strength or great cowardice. He sacrificed his views for his people, he sacrificed his home and standing for Virginia. But, he did sacrifice his morals nether the less.