I'm not so sure that was the case. Lee didn't appear to be conflicted about secession when he wrote to his son G. W. Custis Lee:
I received Everetts Life of Washington which you sent me, and enjoyed its perusal. How his spirit would be grieved could he see the wreck of his mighty labors! I will not, however, permit myself to believe, until all ground of hope is gone, that the fruit of his noble deeds will be destroyed, and that his precious advice and virtuous example will so soon be forgotten by his countrymen. As far as I can judge by the papers, we are between a state of anarchy and civil war. May God avert both of these evils from us! I fear that mankind will not for years be sufficiently Christianized to bear the absence of restraint and force. I see that four states have declared themselves out of the Union; four more will apparently follow their example. Then, if the border states are brought into the gulf of revolution, one half of the country will be arrayed against the other. I must try and be patient and await the end, for I can do nothing to hasten or retard it.The South, in my opinion, has been aggrieved by the acts of the North, as you say. I feel the aggression and am willing to take every proper step for redress . It is the principle I contend for, not individual or private benefit. As an American citizen, I take great pride in my country, her prosperity and institutions, and would defend any state if her rights were invaded. But I can anticipate no greater calamity for the country than a dissolution of the Union. It would be an accumulation of all the evils we complain of, and I am willing to sacrifice everything but honor for its preservation. I hope, therefore, that all constitutional means will be exhausted before there is a resort to force. Secession is nothing but revolution. The framers of our Constitution never exhausted so much labor, wisdom, and forbearance in its formation, and surrounded it with so many guards and securities, if it was intended to be broken by every member of the Confederacy at will. It was intended for perpetual union, so expressed in the preamble, and for the establishment of a government, not a compact, which can only be dissolved by revolution or the consent of all the people in convention assembled. It is idle to talk of secession. Anarchy would have been established, and not a government, by Washington, Hamilton, Jefferson, Madison, and the other patriots of the Revolution. . . . Still, a Union that can only be maintained by swords and bayonets, and in which strife and civil war are to take the place of brotherly love and kindness, has no charm for me. I shall mourn for my country and for the welfare and progress of mankind. If the Union is dissolved, and the government disrupted, I shall return to my native state and share the miseries of my people; and, save in defense, will draw my sword on none. Letter to his son, G. W. Custis Lee (23 January 1861)
Neither was his wife, Mary Anna Randolph Custis Lee, or his sister. They were all outspoken against secession.
While reseaching the contents of that letter I also came across this anecdote that I thought interesting and relevant:
There is another peculiar post-script to the secessionist drama of 1861.Interesting that he didn't join up with "the cause" right then and there.Oddly enough, one Robert E. Lee was living in Texas at that time. Lee had been stationed in Texas on and off for several years, commanding the Second United States Cavalry in frontier skirmishes against Comanches and Mexicans. He didn't seem too fond of the frontier life; he wrote to his wife of living of a "desert of dullness."
With war approaching, Lee received orders summoning him back to Washington, so he departed Fort Mason, in Mason County, on Feb. 13, 1861, for the journey east. But in San Antonio, Lee was waylaid. A federal general from Georgia, who had taken over Lee's Texas responsibilities, had just cheerfully surrendered his men and supplies to Texas rebels who had ridden out to San Antonio (Sam Houston had dispatched the Texas Rangers to try to prevent this, but they did not arrive in time). So Lee, as a federal army officer, was potentially a prisoner in a state (or country) that was preparing for war with the federal government.
Lee donned civilian garb, reminded the Texans he was a Virginian, and was ultimately allowed to proceed (though he was apparently quite provoked by the Texans, who tried unsuccessfully to get him to declare allegiance to the South then and there). He got back to his home in Arlington on March 1 and little more than a month later, took a command in the Confederate army.
The second portion of your reply concerning Lee's actions in Texas confirm the sentiments he expressed in his earlier letter quoted in the first portion of your reply. His actions were also consistent with my earlier reply in that Lee conceived of his duty to his state which was not Texas but Virginia. While in Texas he was not relieved of his duty to the United States since he was still a serving officer.
I do not read Lee as having second thoughts about the right to succeed or the grievance justifying succession, he clearly, however, regarded the step as a last resort representing a real calamity for the nation and its people.
Written in the context of the life of George Washington as described in the biography the letter notes Lee was reading, the sentiments expressed were common at the time in Virginia and in the rest of the South to the effect that the southern states by revolution [Secession] were effecting a "second American revolution" which was fully in accord with the moral justification of the first.