Ridley Scott in his director's commentary for the first Alien DVD, said that Space Jockeys created Xenomorphs as biogenic weapons to fight an ancient war and According to the book "Giger's Alien," the eggs were originally meant to be housed in a completely separate architectural structure, shaped in the form of a massive pyramid. This would imply the previous existence of a native civilization, wiped out by their reverence for the creatures.
One of these has to be the true Origin to the Xenomorphs.