Lee was too close to the top brass and Winfield Scott to not have been privy to at least some of the planning of the relief of Fort Sumter and the intent to hold the fort at all cost. Yet he did not resign as other southern officers had already done. And there is another question for another discussion, Why did all of the prewar army high command, other than Winfield Scott, resign? So Lee's resignation from the army after a lifetime in that army even to the detriment of his own personal business, and his being offered command of that army, had to be based on something greater, something more intrinsic in his beliefs systems than his mear sectional loyalities.
As I said, at the time Lee resigned his commission, he was a newly promoted Colonel because of all the other resignations above him. As that Colonel he was about the only field grade officer of that rank or higher that was fit for field service remaining in the army to be offered command of the field army. Lee had the confidence of the General of the Army, Winfield Scott, which meant that he had not made statements which would indicate he was simpathic to the southern secession or he would not have been offered that command if Scott was as close to Lincoln as things would seem to indicate that Scott was. After Lee resigned that command was offered to a Major, John McDowell.
Yes, Lee said that he could not fight against his Virginia. But other southerners, like Thomas, found no problem in remaining in the army and fighting against his home state of Virginia. So if Lee didn't resign over his sectionism what would you think would have motivated Lee to have given up his entire lifes pursuit?
Another question, Why was Lee's resignation so noteworthy? Why not Albert S Johnston or P.T.G. Beauregard's who was Commandant of West Point at the time. Their resignations did not merit as much noterity as Lee's a lessor ranking officer than them? It was because Lee was at least a non-commital player going along with what Lincoln and Scott was planning as long as it didn't lead to obvert war. But once Fort Sumter occurred and Virginia announced its intentions to Seceed, Lee had to make a choice. I believe that this choice was that he felt that actual War against the States, even Virginia, was unconstitutional, and that was Lee's reason for resigning.