I don't think it would be seen as mockery by more than a few extremist elements. Jesus having ET origins is an old theory. I just don't think it fits the Engineers, though.
Since we're dealing with giants, if they want to specifically work Biblical legends into this, it would be better to go with the 'Book Of Enoch', which is the part which dealt with angelic representatives of God being sent down to overlook and guide our species, but succumbed to a desire to breed with human females (which could be perceived as a innate curiosity to try genetically modifying us, rather than be hands-off), which resulted in the half-human race of giants known as Nephilim. It even lists, by name, about 200 of these disobedient 'Watchers' and also their leaders.
This was meant to have been the reason God attempted to repeatedly unleash genocide, yet try to also save some of us: These hybrids were getting too numerous and screwing up whatever the plan was meant to be.
Stuff like that would fit what was depicted in 'Prometheus' a lot better than the idea about Jesus which Ridley Scott came up with: The reason they were going to Earth, was because of a prior directive, way back when, to take out a rogue group which had set up on Earth and were empire-building without being given authorisation. Not because they detested humanity, itself, but because some operatives were doing their own thing and considered dangerous.
The tale of the Watchers is genuinely quite fascinating and outlines how they gave humans (I think females, specifically) knowledge which we weren't meant to have, right from cosmetics to warfare.
There are a lot of tales of giant beings, supposedly descended from people who came from the sky, which could very easily be worked into this. Especially from the native Americans, who regularly faced off against a race of red-haired cannibalistic giants.
