A Spanish-Language documentary on Netflix titled "Los Ninos Heroes de Chapultepec" features a collection of three Mexican and one American historian discussing the Mexican American War of 1846 to 1848. At one point, the American historian, John Mason Hart of the University of Houston, responds to a question about American attitudes during the war.
He says that "Some had very aggressive thoughts. Robert E. Lee, the future Commander in Chief of the Confederacy in the South during the American Civil War, wrote a letter that is now in Pennsylvania, saying that Mexicans should be thrown into the sea so that they could make this magnificent country our own."
I found this claim very surprising. It changes my whole image of Robert E. Lee and casts it into quite a dark perspective.
Can anybody here shed light on the letter that Professor Hart cited? Did Robert E. Lee really express such a sentiment?
I'm afraid I can't address your main question vis a vis Lee's attitude toward Mexico and Mexican or Hispanic people, but I do have an old write-up that touches on Lee's attitude towards slavery and people of African descent. It might help you to get a better grasp on Lee's mindset in general, and aid in understanding why many of the narratives that surround Lee's career try to downplay or hide that 'dark perspective' you speak of.