I would personally prefer the story to have a looser connection to Alien. The Space Jockeys are a race, not an individual being. There should be more than one ship, and more than one of their kind. Prometheus could well be a film which simply shows one group of humans making contact with one such ship and encountering a living member of that alien race, and in doing so we learn through them the nature of this alien race, their motivations in space, and the purpose of their ships.
By doing that, Prometheus can tell a complete and self contained story without being held to the timeline and details of Alien, while also giving us additional context as to why the ship on LV-426 might have been there, and why it was carrying Xenomorph eggs.
I agree with this; my comment was about whether the question would be resolved or not as to whether that ship was the same from Alien. Regardless of the answer, I don't think it will be left ambiguous.
I'd prefer your scenario as well, as it would add context and history to Alien, without tethering Prometheus to the particulars; it would fill in the history without entirely sapping Alien of its sense of mystery.
I don't think that's what we're getting, but I would like to be incorrect.