One thing is certain, "The Company" never has had a history of lying...
FWIW Josh, I read your review at the other site.
You bring up some valid points, most particularly that the actions of the scientists were as scientific as the actions of my kittycat.
IMO, this is the one major flaw in the movie.
Many of points you have raised in the review have since been answered by the posts of others here and elsewhere.
Although not a masterpiece, Prometheus is a fine (and stirring) sci-fi.
My 8 farthings.