I can immagine the theory has probably crossed several minds through time, but most who where smart enough to consider the theory where probably also smart enough to keep it to themselves. And those who didn't probably ate their words under torture or got executed. Most cultures had some sort of spiritual belief entangled with the leadership, and a lot of them involved animals and their origin. So claims that didn't fit into the current belief would be a threat to the power of the current leaders.
Which is probably also why Darwin had to be so thorough, he had to be 100% sure about what he was saying, and explain it in a way that would convince people beond the shadow of a doubt. He also chose the right title I think, "The origin of SPECIES", not the origin of life or the creation of anything, he only explains how the diversity of the current species came to be. This way he doesn't completely destroy the concept of faith or creationism with his staments, since religious scriptures are open to interpretation, I mean even the story about Noah was pretty far out before Darwin and his theories, and I'm sure many christians throughout time have asked themselves why they couldn't marry their sister if everyone descended from Adam and Eve anyway... anyway he tries to attack faith as litle as possible while unraveling a big part of the mystique that most faiths made bold claims about.
But I can immagine he must have felt one hell of a chill whenever he handed in that book to a publisher or a university or wherever it ended up first
There is no way I would ever have had the guts to do something like that, I mean I'll open my mouth and be a litle too honest on occasion when drunk (And almost always at the wrong time and place, directed at the wrong crowd), but to flip the church off like that in the middle of a chistian country... well I don't think they had drugs strong enough to make me do something like that back then.
(I won't be reading it though, I'm sure it's facinating, and maybe if theres a resumé somewhere... point being I rarely finish a book, I always... wonder off subject... I'm also horrible at explaining things)