I'm not against the Space Jockey being involved in human life--I mean, it had to have been, considering its basic anthropoid shape and five fingered hands. If they went in the opposite direction and said it's just another alien species, that would be some stupid Star Wars crap. This isn't fantasy, it's actual sci-fi, and those five fingers need an explanation.
I'm just worried PROMETHEUS will end up being not-so-good, in a STAR WARS prequel way, and retroactively taint the original film and series, and that certain plot turns it takes will cheapen the original. I'm cautiously optimistic, though.