Bourn's defensive stats are significantly better defender than Ellsbury, but besides that your points are spot on.
The other factor was that there were such a large number of outfielders available last year, and many of them were quality center fielders. Victorino, Bourn, Upton, Revere, Pagan, Choo was traded as a CF, and even Drew Stubbs has given a solid WAR. That's a lot of options. With Choo likely moving back to a corner, and Granderson probably taking a pillow contract, Ellsbury will be the premier CF.