If I recall correctly, the oldest star-map was left 30,000 years ago in the British Isles. They obviously didn't want to destroy the human race back then, it was a decision they came to at a later date. Most likely, the site wouldn't have been a death-trap of dangerous bioweapons and terraforming shit had they not intended to kill us 2000 years ago. We would have eventually found our way there, and there would have been living Engineers to greet us.
The larger questions are about why they changed their minds, why they wanted to destroy in the first place, and why they didn't clean their fucking mess up. They need only activate the same ship after everything on-board was dead (wait 6 months until all the monsters starve to death?) and the mission could have been completed. Unless there was literally a civilization wide cataclysm that took place, there would have been others out there who knew about the mission, and could have continued it with only a slight delay. That's assuming they don't have other weapon stockpiles laying about to send in its stead, and different ways to engineer an apocalypse.
As I stated previously, we don't have to assume that all decisions were made by a unitary alien government that controls all the engineers. They can have private initiatives too, they can have multiple independent political bodies too, they can have individuals acting on their own too. This applies both for the creation of humans on Earth and also the destruction. One of those things, or both, could have been the actions of governments, individuals or private enterprise on the part of the aliens. The same aliens who made us aren't necessarily the same that wanted to destoy us, and so on.
The fact that they never bothered to "clean up" the site to get rid of the dangerous stuff lying about points towards either that base being secretive (only the people that lived their knew about it), or there was an aforementioned cataclysm that destroyed much or all of the space-jockey civilization.
