There's still a lot of unanswered questions in the Prometheus franchise, but here's what we do know:

 - The Engineers seeded at least some form of animal life on Earth and/or other planets, including humans (though plant life was already present on whichever planet we saw in the opening sequence).
 - They're a ritualistic society that has at least a pseudo-religious culture.
 - LV-223 was a military R&D outpost where the Engineers were engaging in bio weapon research, namely [Chemical A0-3959X.91 – 15][1], which was also used to seed life on other planets.
 - At some point, the Engineers lost containment on one of their experiments, resulting in all but one Engineer being killed.
 - It is strongly suggested that the Engineers had decided to attack Earth long before humans arrived on LV-223. Scott has said that, in an earlier version of the story, this was supposed to be a result of humans killing "Space Jesus," which the Engineers had sent to Earth in an attempt to redeem mankind. In [the same interview][2], Scott says *Paradise Lost* was part of his inspiration, in which case the Engineers would be analogous to the fallen angels who try to corrupt Earth/humanity after losing their war with God.

With all of this in mind, it doesn't appear that the Engineer suddenly goes crazy so much as he was just behaving based on his described nature and motives. Whatever reasons the Engineers had for leaving clues on Earth pointing to LV-223, the Engineers that we see in the holograms (including the lone survivor) were not the benevolent gods that the crew were seeking. Waking up the surviving Engineer did nothing to change his mind about destroying humanity.

Perhaps in the distant past, some Engineers had a benevolent view towards their creation, but the ones shown on LV-223 clearly didn't/no longer shared that sentiment.


  [1]: https://avp.wikia.com/wiki/Chemical_A0-3959X.91_%E2%80%93_15
  [2]: http://www.movies.com/movie-news/ridley-scott-prometheus-interview/8232