Fiffield says that the scene in which a pile of dead engineers appear to have been ripped from the inside reminds him of a "Holocaust painting!" Now at the time for some reason i immediately though of world war 2. But the truth is the term Holocaust has been used to describe religious rituals and sacrifices made to the gods in which the bodies were completely burnt.
This leads me to believe that those dead engineers were sacrificed to the big head in the urn room. What this also leads me to conclude is this: The chestburster (both the engineer's life and son represented) is extracted, burnt or melted, or his genetic material is collected somehow and he is put in stasis with the bioformer (simbolizing one's immortality, through death one becomes new life) . It's basically the concept of afterlife, where he will truly be reborn as something new, the perfect being.
What i think happened, was that somehow one of those chestbursters got loose and grew up (or maybe several), and that is why the temple was mostly dead.
EDIT: oh man, and this leads me to conclude something even darker. Either they are being lied to, and don't know about the underground ships, or they are weaponizing themselves on purpose. Each one of those Urns is a dead engineer, and the ship is full of them. Mass ritualistic suicide.