Remember the iPod and iTunes Music Store? Customers were free to download and install music on their iPods, but the iTunes Music Store was still a runaway success. Same would be true for the App Store.
@cleverdevil I'm of the same mind. I know I would put a lot more trust in the App Store than a 3rd party and value a one-stop shop. I'd make some exceptions but the App Store would always be my default.