What is this obsession with the Jockey being some kind of an infection thing?
I'd bet good money the tall man IS The Jockey. He goes into the suit and pilots the ship. He, or one of his kind, is seen at the dawn of time.
My bet is the Jockey unleashes the creatures on the crew when he's disturbed, the crew awaken them when tampering with the suit/corpses, or trigger an automated system when entering the ampule room.
I don't think there's any major twist in terms of the Jockey. I know a lot of folks want to believe we're going to see some Lovecraftian Cthulu Old one thing that comes out of the dark, but I honestly believe the large humanoid who is seen raising the control console, and on board Prometheus in the trailers is The Jockey/Engineer.
As far as Weyland goes, I could see David maybe having such a fascination with what they encounter on behalf of Weyland, and perhaps be compelled to expose some of the crew to it on purpose also by Weyland's command. (Very fitting with what took place with Ash).
I guess my point is don't push so hard for what you expect or want to see. Let the unexpected and the different be okay. A lot of people seem to have already set themselves up to be disappointed, not because what Prometheus is going to do is necessarily bad, but because it's different from what people expected.