The engineer they are facing, might not be our Prometheus (if the theory is sound).
If he was subjected to horrible punishment by his own kind for his crime, he might be long gone by the time Prometheus arrives on the planet.
Who knows... could the 'accident' aboard the inside the temple, potentially wiping out most of the crew, be attributed to them fighting eachother? 'Prometheus' vs the rest? Could he have unleashed the havoc intentionally...?
Getting ahead of myself here I think... Better go shopping - my mind works better when I'm spending
(besides, it seems like AvPG is having tech issues right now)