In my estimation Lee's quote was the "Polite" explaination for his resignation. But carried the importance that he believed that Virginia was correct in it stance.
I don't believe that you could have MADE Lee do anything which he was not convienced was not right. Had Virginia been wrong in his mind I do not believe that he would have left the army. I don't believe Lee, being the man that he was, would have joined the Confederate Army even if he did resign his commission in the United States to keep from fighting against his home state, if he believed that it was wrong and against his principals.
In his position Lee could have probably requested and recieved any position in the US Army that he wished. If he had wanted to have stayed in the United State Army, and not actually fight against Virginia, he could have requested the Inspector General office since Samuel Cooper had resigned. Or he could have requested a post in the far west away from the War.
Lee, in my opinion, was one of the few people who truely could have chosen what he wanted to do. BUT, he saw his duty, his most sublime word, as serving Virginia. WHY?
"No man should desire to do less than his Duty" ...R.E. Lee
So in his resignation Lee effectively said that he was following a higher "DUTY" than his oath to the United States government, which he took very seriously. Contrary to what our Northern friends might say.
Now if he were following a HIGHER duty, What was that duty? Was it mearly to exchange one government for another? Was it simply to exchange his loyality to the United States for a loyality to Virginia?
I don't Think so. Lee was a much deeper man than that.