Until what happened to the crashed derelict in Alien is explained onscreen, on film, and made official....I don't think you can take anything Ridley says as canon. It's fun to speculate and guess, but to me, until I see it fleshed out on film, we still don't know the story behind the derelict just yet.
As for the Aliens...based on the mural, they do exist before the Deacon is born. I'd say the Deacon is a new distant cousin of the original Xenomorphs, which we haven't seen yet. This is just a theory, but maybe the Aliens already exist. They were created by the engineers to wipe out planets. BUT....what if they were designed to be asexual and couldn't breed? That way, they can kill off entire planets then eventually all die off themselves. The engineers then started f**king with their DNA, reverse engineering them, and making a way for this black goo to turn any living being into a Xenomorph--think of the concept taken from William Gibson's unused script for Alien 3 (where the Alien DNA goes airborne, infects people and turns them into Aliens). What the engineers never anticipated is what would happen when the Alien DNA/black goo encountered a female human being for the first time. We all know that the Aliens take on certain characteristics of their hosts (ie: the dog Alien from Alien3). Well, when Holloway got infected, maybe his now alien-human sperm got Shaw pregnant and implaneted a xeno-embryo of some sort. That embryo latches on to Shaw and is basically introduced to the human reproductive system for the first time, that embryo of course starts taking on those attributes (like the Queen in Resurrection) and Shaw gives birth to the first proto-Facehugger, giving the Xenomorphs the ability to breed. The Alien DNA strain now has the ability to pro-create. So maybe the Deacon will end up becoming a Queen and eventually evolving into the breed of Aliens fromthe first film. Maybe tthe events in Prometheus mark the beginning of the new Alien lifecycle.