Little Newt, thank you for this type of question.
The context of what Ridley Scott was saying in the quote you cite was in relation to an attack on LV-223 shown in Prometheus around 2000 years ago. He, Ridley Scott, made the connection with the putrid state humanity was in at the time during the last stages of the Roman Empire.
This concept has been discussed many times by many talented contributors. Gareth and BigDave covered this topic in 2013.
"If you look at it as an 'our children are misbehaving down there' scenario, there are moments where it looks like we've gone out of control, running around with armor and skirts, which of course would be the Roman Empire. And they were given a long run. A thousand years before their disintegration actually started to happen. And you can say, 'Let's send down one more of our emissaries to see if he can stop it.' Guess what? They crucified him."
Ridley Scott
The Romans crucified Christ. The connection I made was that Ridley Scott chose that a single (Jesus') crucifixion was very, very bad during the time the Roman Empire was known very well for how often they crucified people for many different reasons. The crucifixion machine was well oiled and up and running during the Roman Empire and Ridley Scott segregated one single crucifixion as different from the rest of the many that were crucified 2000 years ago.
BigDave is correct when advising caution with direct links to Jesus' crucifixion. The Prometheus events up to the Alien: Covenant released material shows traits from different cultures and religions.
The attack on LV-223 about 2000 Years Ago

Someone interceded on humanity's behalf to stop the Engineers on LV-223 with an attack that killed them (shown below).

With the loose connections to Christian history concepts and the more firm connections the Nephilim Giants progeny story (the Ancient Aliens TV program loves to cite this) , I speculated that maybe the black goo was divine and the Nephilim that intended to attack humanity (Engineer plan to destroy Earth unveiled by David 8 on LV-223) was disrupted by Watcher angels.
The Nephilim are the children (Giants) of the Fallen Angels in the Bible that polluted the gene pool of humanity and brought on the cleansing flood spoke of in the story of Noah.
I thought with these connections, is the third party that attacked the Engineers on LV-223 Watcher Angels?
“When men began to multiply on the face of the Earth, and daughters were born to them, that the sons of God saw the daughters of men that they were fair; and took them wives of all which they chose.”
Genesis 6:1-4
The below quote is from a deep article on the subject discussed here.
"In the esoteric Luciferian tradition they were a special elite order of angelic beings created by God to be earthly shepherds of the first primitive humans. It was their task to observe and watch over the emerging human species and report back on their progress.
However they were confined by the divine prime directive not to interfere in human evolution. Unfortunately they decided to ignore God’s command and defy his orders and become teachers to the human race, with unfortunate repercussions for both themselves and humanity."
http://www.newdawnmagazine.com/articles/enoch-the-watchers-the-real-story-of-angels-demons

Did "angelic beings created by God to be earthly shepherds" wipe out the Engineers on LV-223 because they were doing their job?
Were these earthly shepherds looking out for humanity when the descendants of the Fallen Angels (Engineer, Nephilim Giants) meant to destroy Earth?
