I read the Ata'mal crystal's history and nothing state it was a gift from naaru. It's history is in the dark.
"During the draenei's journey, the enigmatic naaru race blessed them with Light-given knowledge and power. The naaru explained that there were other forces in the cosmos that would stand against the Burning Legion."
If Sargeras was able to change a race by using his fel magic, naaru can change a race using holy magic.
"The revelation that they are an offshoot of the eredar was bewildering to some fans, as was the idea that Sargeras corrupted the eredar as opposed to the other way round. However, while Sargeras's corruption of the eredar is a retcon, it should be noted that the draenei-eredar relationship is not. Except in the case of the lost ones."