Here is a quote from near the end of the NYT article (hope it's not so much the NYT copyright stormtroopers come after me):
Dr. Marean of Arizona State University said that in the bone tools archaeologists were seeing a new picture of modern human evolution. "This puts the behavioral evolution in step with the anatomical evolution," he said.
It's a bit of an understatement to say the article isn't overturning evolution.