I hear you on both the way the supposed Religion-mix came across as really Christianity and some tiny nods. I didn't have the impression the message was to be "faith is for losers"; if any ST episode has that one, I'd go for "Who watches the Watchers", or however the episode in which Picard accidentally becomes a god to the Mintakans was called. If anything, I had the impression this episode sold science short not just by juxtaposing it to religion - which as you say isn't true for a great many scientists throughout history -, but by making Jacob the sole embodiment solely due to his heritage. Didn't in 200 years any other research- and invention-minded folk exist? Curiosity and practicality should have produced far more of them.

Mind you, it's entirely possible that the context in which we watch the episode makes all the difference. I mean, it took me over a decade to realise that the DS9 episode in which Winn first appears, where she organizes a protest against Keiko teaching about the Prophets as Aliens in the School, was a sci fi take on the US still having trouble with evangelicals vs Darwin. (Then, and today it's climate change deniers and anti-vaccine people, I suppose) The reason why I was missing this context was because arguments about evolution theory in school just didn't happen in Germany of the early 90s. (Now, arguments about cruxifices in school, otoh… But seriously, the most Catholic and the most Protestant of schools would not have had a problem with teaching about Neanderthals. Not least because the actual Neanderthal near Düsseldorf is a tourist attraction today.)

Burnham & Pike: agreed.