ok last one,the pile of engineer corpses in prometheus

I would say they were running from something (the hole on one of their chests confirms a Xeno or Deacon outbreak) and just piled up in a panic, much in the way that insects do. Just my guess anyway. 

That's what I've thought some sort of mass hysteria.When David activated the hologram,it shows the engineers running away from something(possibly xenomorph,who knows)and lock themselves in the anticamber with the vases of black goo(why they thought that that was a good place to hide i dont know,and where did the ones that made it in go).The ones pilled up may have trying to get in somewhere else and sort trampled each other to death.On the other hand your theory about corpse disposal might be closer to the truth(Did one them point out it look like something burst out of them?)Plus Fifield said it looked like something out of the holocaust.

In the Fire and Stone comics an Engineer alone dragged hundreds of Xenos into a pile. Which could imply that if they were being picked off, they just tossed their fallen comrades into a pile. 

Though both of your theories are easily possible too.

Maybe they didn't lock themselves in. Perhaps they were locked in to prevent getting out.......

@dk *x-files theme plays*

Good point

The bodies were actually stacked in front of another door, to another room, similar to the Ampule room the crew initially investigate. Either fellow Engineers piled up the "infected" bodies, or whatever hunted them did so, as a means of "hoarding" or congregating hosts.

The Ampule room which the hologram shows the Engineers running into had no visible "secret back door" or way out. However after re-watching Prometheus - the hologram shows the last Engineer getting killed at the door's entrance, but no indication that the door shut before letting whatever was hunting them, into the room, with the other Engineers.

I believe the piled bodies are the remains of those in the hologram, who were unsuccessful in closing the door to the Ampule room and who were slaughtered and dragged to a different room entrance by whatever Alien monster was capable of doing so. The Engineers never had a chance to hide or plan an escape - the Alien hunter was too fast.

Actually,I suppose the black goo had something to do with it,as Shaw said:

"Ask him where they're from.Ask him whats in this cargo.It killed his people."

Some guy from the making of Prometheus commented that whatever happened to the engineer's head that they found in the pyramid (it exploded) will happen to Fifield at some point,he's losing himself to an alien within him.

Soo Fifield was an example of what would happen to us if the engineers released the black goo 2000 years ago if they didn't lost control of it,and I think that he is also an example of what happened to some engineers that were infected with the black goo.And some that were infected were either trying to kill themselves before they became fully mutated while other engineers were running away from them to the safety room.

For the pile of corpses,Idk they are probably those infected ones who were unsuccessful in getting inside the room or whatever happened to them.In Jon Spaihts' script,those engineers were struggling/begging to get inside the room but were eventually chestbursted.

And how comes they are wearing the spacejockey masks? Isn't the mask part of the cockpit and only attached when strapping into the cockpit?

I assume the Engineers had spacesuits, including helmets, when they were outside of the ship exploring planets. 

@Stan Winston (deceased)

It looks like it attaches to the  chest piece. Great way to avoid getting facehugged if the suit is acid resistant.