Naughty dog will do well. In past many people have left them and made their own studios. Plus they really leaked a lot of talent before original uncharted.
I think an even bigger thing to understand is that she was only there for a bit over a year. Zero involvement with Uncharted, Uncharted 2, Uncharted 3, and the last of us. ND was perfectly fine without her.
Also more likely is that she finished her main job. She was brought on to port Naughty Dog over to PS4 development. A project like that is never complete as there is always more and more power you can squeeze out of a system, but I imagine the bulk of it has been figured out.
