What if the atmosphere is not only getting in, but also coming out of the temple once the ampule room is opened? When exactly did they notice they could breathe in the temple. What is the temple doing pumping air, I mean obviously it's for the Engineers to breathe, but maybe they were affecting the atmosphere in the first place. Weyland figured it out with a similar design. Could these be ancient atmospheric processors? I think what results from them opening the door wasn't a trap...
It all goes wrong because of the battle the Engineers were engaged in and how they suddenly sealed off the door, decapitating the one Engineer, causing the improper shutdown. leaving the atmosphere outside only partially converted. It was reacting to the change in atmosphere but mainly the sudden presence of oxygen in that chamber. I think this was a chamber that's part of the system and intended to alter the atmosphere, but the way they left the temple partially running, & pumping out oxygen affected this chamber when it was finally opened. The sudden change from outside, now that the planet has returned to it's normal atmosphere, caused the sudden degradation. It wouldn't be a problem if the thing had been shut down before being sealed off, or if there was no oxygen present in the rest of the temple to rush in. Also causes the sudden restart of the ancient atmospheric processor when the doors opened, which could be powered by one form of the life altering substance.
So, the actual atmosphere outside begins to change.. which was in the process of being converted for use by the Engineers, and is now partially being processed again. However it all malfunctions at first, because the air outside has returned to normal over the 2000 years. The weather picks up and this causes Janek to warn them of a sudden, huge storm approaching. The humans/engineers can breathe in the temple, and I think David messed everything up, made things degrade because of the state the Engineers left the facility in. But he also made it so the air outside started being converted again. So does it generate oxygen and atmosphere, possibly even the first stages of plant life to make the planet habitable by way of some form of the magic goo in a more controlled form? I guess what I'm saying is does this thing mine/convert the toxins in the air into something they can breathe or use if concentrated and mixed as a weapon? Sort of a parallel to what the flamethrower does to produce fire.