But even today, I think many people do not understand the philosophical implications of evolution. Daniel Dennet wrote a whole book on this: "Darwin's Dangerous Idea" (which, perhaps you're familiar with). I think Franklin would have been shocked at evolution's explanatory power. It's hard to talk about things like emotions (anger, lust, jealousy), ethics (justice, retaliation), medicine, or even sexuality without invoking genetics and evolutionary theory.
I agree with you that evolution does not (and cannot) disprove the existence of God (or gods) or even that we were created 6,000 years ago (maybe God created the world to look as if it's ancient).
But I think Franklin would see that evolution has shrunk the numinous realm down to a very small box, and I think that would have shocked him.
Life, though - that system and its output, holistically - still lacks self-evident purpose. (Which is not to say that it must have one.) Why was this function written? Is it merely the output of a higher-order function? (Involving cosmic turtles?)