In the origional screenplay which was leaked, it said the eningeers would terraform lifeless planets and create life in their own image. LV_223 was in the process of being terraformed, but the eingeers found an existing life form. In the sequal we probably will findout, LV_223 was a terraform gone bad. Where a hostile life form that existed there, hijaked the engineers lifeform.
The worms which grew to a cobra, infected the Engineers. That's no bio suit the engineer on LV_223 was wearing, it's an infection of his DNA like Halloway. The worms also infected Halloway and Shaw's fetus which will become the Queen Xeno. Once the black gue gave the worms on LV_223 the power to infect and reproduce thru the engineers, it changed the population of engineers on LV_223 to the dark evil engineers. That's why they worship the facehuggers. They are infected by evil. They are not real engineers anymore. They are Fallen/Dark Angels.
The one suttle difference in the Engineer on earth and those LV_223 which are infected is, the engineer on earth is peaceful, also it is white, and performing sacrifice to give life. It creates life ! The infected evil engineers on LV_223 are dark, infected by evil, and they are out to destroy earth because they want to spread their race. Shaw has mistaken the evil engineers as her creator instead of the real engineers which she has not met yet (sequel).
I am pretty sure in the sequal, when Shaw goes to the home planet of the engineers they will be white and friendly and good, that is if they have not been also infected and destoryed by the worms mutation and facehuggers as has already occured on LV_223 . Or maybe Shaw will infect them by taking a spaceship with worms to the engineers planet. (intersting twist, meeting your makers, and destroying your maker in doing so).
The fact that the crew found no life but 1 evil engineer, shows the worm race is so destrcutive that it infected and destroyed all the engineers. Question is has the locus that is the worm race already destroyed all which the orgional engineers created? are we all that is left from the origional engineer's terraformed planets?
Well, that's what I think the sequel will reveal, that shaw did not meet her maker the GOOD engineers in Prometheus. :-)