I don't think Microsoft is planning on running their own app store (at least not with the Kinect), but like with the iPhone, users "voiding the warranty" so to speak may usher in a wave of innovation in terms of accessibility and user interaction beyond the Xbox. Microsoft should know that watching what people do with the Kinect outside of the (artificial) design limits is one of the best (and least expensive) form of product-market research.
Here's an idea for use that Microsoft could create and profit from: Kinect as a remote control for a media center PC. No more losing the remote or replacing batteries. That one's free, Microsoft.