Okay, this is what really happened:
When you get right down to it, the Ancient Wanderers did not really create the Protoss or Zerg. The Protoss evolved on a planet engineered by the Xel'Naga, which they left alone after seeding it with life. Years later, after all of their experimentations failed, they returned to Aiur to see that a highly advanced race of creatures evolved. Semi-sentient creatures, they were hunter-gatherers that lived in tribes dominated by warrior rule. With their findings, the Xel'Naga began to slowly tamper with these creatures, and eventually rose them from semi-sentients to a thriving civilisation. Since these creatures were the first of their experiments to rise above the feral world, they were given the name Protoss, Xel'Naga for "First Born".
At this point, the 'Naga were thrilled with their creation, and introduced themselves to the Protoss. In such awe were the Protoss that they heralded the Wanderers as Gods. Over time the 'Naga integrated themselves into Protoss socieety, and taught their Aiuran children. However, as the decades passed, some Protoss began to speculate as to what the Xel'Nagas' intentions really were. Slowly, as rumours spread, the Protoss began to shy away from their Creators. And too, the Protoss society began to fracture, and the tribes withdrew thremselves from each other as the individuals became more individualistic. So, the Xel'Naga made to depart, believing that they had corrupted the innate purity of their Creation. Upon hearing of their departure, the Protoss attacked the 'Naga out of fear and anger. Many Xel'Naga were slaughtered. With the fear and hatred still coursing through the Protoss, they turned on eachother in despair. Thus the start of the Aeon of Strife.
The Xel'Naga wandered into the core of the galaxy, recognizing that the rise of the ego was what marred the purity of the Protoss. They found a world called Zerus, upon which they found insectoids called Zerg. They began to focus their experiments on these Zerg, evolving them so they survived the harshness of the fiery world. Over time, the Zerg evolved the ability to burrow into the flesh of other creatures and control them. The DNA of these hosts was slowly incorporated into the Zerg gene pool, giving rise to a plethora of different Zerg breeds.
Remembering their folly with the Protoss, the Xel'Naga took the intelligence and consciousness of all Zerg and forged a new being from it- the Overmind. This was the incorporeal manifestation of the instincts, drive, and thought of the entire Zerg race. This creature became self-aware, and eventually discovered the existence of the 'Naga. It severed its psychic link to its creators. The Xel'Naga were now in a state of panic. "What is going on?!" Not too long later, they would see millions of Zerg rising from Zerus towards their fleet.
A good portion of the Zel'Naga race was slaughtered or assimilated into the Zerg. Only a few World Ships escaped the massacre.