My take on it (having seen the movie a second time now), is that the movie being more on-the-nose about the cause of the Engineer's wrath was a consequence of earlier (and poorer) drafts but was deliberately moved away from for a bigger purpose than just feeling too on-the-nose or the rather silly claim that they were afraid of offending anyone. I think that watching the movie, it is clear that they "reason" for their wrath cannot be definitively assumed from anything, including Ridley's comments. I think it has to be considered still open ended; once they decided to set the movie up for a sequel, they explicitly have Shaw going off to get the answer. David even says that it is not important, but Shaw says it is to her because she is human and he is just a robot. So at this point it isn't Space Jesus (but it still could be in the future). So in summary, I don't think they intend for the audience to understand it yet, nor do they expect you to have to read outside material to understand this part. I think it is unanswered on purpose.
Apparently there is a whole conversation between David and the last Engineer that was cut from the film, maybe they discuss some of this there?
Also apparently there is a fight scene between the Engineer and Shaw (with the axe) on the life boat that they cut because they thought it was too unbelievable compared to him easily killing the other crew earlier, but I would like to see that fight in the deleted scenes.