There's no need for all this speculation on Lee's reasons for resigning his commission. He stated his reasons quite clearly in his letters to various family members and friends. The letters are very moving and introspective, and, above all, painfully honest -- Lee was not one to equivocate. Check "Recollections and Letters of General Robert E. Lee, by Captain Robert E. Lee, His Son." Chapter II covers his correspondence regarding his resignation and his reasons therefor.