All I can think about a Lee Presidency would be that the North may consider to secede since Lee wouldn't make a move to end slavery. He appears to be one that would let the states decide. Which leads to the possibility that:
1. The North wins its independence and becomes a sovereign state.
2. The North rises in revolt against the South, essentially a war against slavery, which it throws off the South and then proceeds to invade the South to eradicate slavery. This essentially destablizes the concept of peaceful governance, tho it follows through with Jefferson's idea of periodical revolution to keep democracy strong.
3. The North waits out Lee's term(s), and strives to win the next national elections. Civil War delayed.