There is a big difference between the Valley of Virginia and Tidewater on the one hand and that which is west of the Valley. The Valley remained supremely loyal to the Confederacy and it was that to the west of it which broke away. The Valley was peopled by German, English and Scotch Irish stock and, to the west, the Scots and Irish predominated. The geography to the west compelled a different lifestyle than the great rolling hills of the Valley. Slaves were useful to some degree in the Valley, although not nearly as much as in the Tidewater, and not so very profitable in the harder scrabble Farms of the western mountains.
It is a further peculiarity of the area that the geography tends to run northeast to southwest, a geographical feature which Stonewall Jackson and Jubal A. Early were able to capitalize on in 1862 and 1864. Lee used the Valley to cover his invasions of the North in' 62 and 63. Militarily, the Valley would tend to run a northern invader out into the western mountains where he was relatively out of the game. But A Confederate invasion of the North would erupt into Maryland and Pennsylvania threatening Washington, Baltimore, Philadelphia and Harrisburg. So it was easier to reach Pennsylvania that it was West Virginia because of the mountains. Finally, the passes across the Blue Ridge into the Tidewater were key to strategically exploiting the military geography of The Valley.
Robert E. Lee was very much a product of Tidewater Virginia. His wife was a descendent of Custis Washington and Lee himself was descended from King Carter, the richest man in Virginia of earlier colonial days. His father was White Horse Harry Lee whose eulogy for George Washington, "first in war, first in peace, first in the hearts of his countrymen" betokens his intimate association with the first families of Virginia until he fell on hard times. Lee's boyhood hero was George Washington. These were the Virginians of the plantations and they had not so much in common with the people of the Valley with whom Stonewall Jackson had closer associations. The Tidewater Virginians like Robert E. Lee had even fewer associations with the part that broke away to form West Virginia. There were ethnic, cultural, religious, and lifestyle differences, all dictated by the geography I described above.
So to speculate as you request, I do not think that foreknowledge of West Virginia's breakaway would have influenced Lee's decision to tender his sword to Virginia.