An excellent argument here. My personal view regarding the pioneering techniques displayed in The Birth of a Nation is that even if they weren't used here for the first time, they were used most effectively here for the first time. This is often true of groundbreaking cinema. Young Sherlock Holmes features the first use of CGI, but it isn't until we get to the likes of Terminator 2 and Jurassic Park that the techniques are widely celebrated.
I have always taken Martin Scorsese's view of Intolerance, in that it is a plea for tolerance. However, as to whether it was Griffith's plea for tolerance of what he'd done with The Birth of a Nation, I have no idea.
Regarding your other points, they are spot-on. The Birth of a Nation was immediately controversial. People protested it from the very beginning. Within it's own cultural context it was already offensive. Gone with the Wind is a civil rights sermon in comparison.
As for Lillian Gish, I can't believe she was that oblivious either. That just seems ludicrous. How can you star in a film featuring white people made up to look black, that features the Ku Klux Klan emerging as a heroic group of people, and not realise what you're starring in? It doesn't wash one bit.