Yes, Lee expressed many diffrent opinions before, during and after the war as he thought it best served the people of his region. He definitely did not want to see a protracted, informal period of warfare.
Lee was trained to do his duty, and he was often painfully conflicted as to just what his duty amounted to under drastically shifting circumstances. When he thought it was his duty to protect his Southern slave master heritage, he did. When he thought after weeks of agonizing contemplation that it was time to actually fight for his region, he did. And when his side lost, he took defeat hard but without bitterness.