There are lots of oddities in this movie, but an informal poll of a few people comes to the conclusion that the person who sacrificed himself at the start of the movie was a rogue or at best, anti-military actor, bent on seeding life to another planet. It also could have been a separate faction hedging their bets that the bioweapon facility on the planet-or whatever the mission of the military people-was going to be too risky. Therefore, spreading life, or at least the building blocks of it, to other planets far, far away made sense for the survival of their species.
Another thought is around the idea that one wakes up a 2,000 year old warrior expecting them to help is a bit egocentric. They didn't know what they were going to find on the planet, but once there, it was clear it was some sort of military base; whether more for research or defense or offense doesn't really matter so much. The humans assumed they were so important that they could get the 2,000 year old being to help them without offering much of anything in return is just egoism. A warrior now awake, and if properly trained, will continue on their mission without letting themselves be exploited by these small beings in front of them.
The other human egocentrism is that this entire base existed to kill them and wipe out Earth. Maybe the Engineers had other enemies to worry about and Earth was some backwater they weren't even thinking about for destruction, just colonization or resource extraction.