Your theory is a bit flawd since the movie ended up with a r rating.
And just because he said 20 years ago he was thinking the eggs were for a war it doesn't mean the engineers were fighting between them. Back then he could have meant they were fighting other species. And by how things turned out in Prometheus it could mean that is the way the engineers dispose of their creations/experiments on all the different planets where they have been. At some point they had the eggs, in time they could have perfected the technology and used goo, or the other way around.
After they showed us the engineers in this movie, i believe they are not the kind of species that fights with eachother. Just a personal opinion but i don't think they like the idea of hurting eachother but more likely they all live in peace and work for a common goal. The last dude seemed displeased when Shaw got hurt by the bodyguard.
And to make the engineers have different factions and introduce a civil war,imo could be kinda cheesy