While there is a growing trend for newer apps to adopt the Mac App Store as their exclusive point of sale, most established developers who have gotten into the store are maintaining separate versions of their apps. And even some of those who are going Mac App Store only, such as Pixelmator, are still offering demos of their apps via their company sites.
It's worth keeping in mind that though many customers may to transition their existing licenses into the Mac App Store, there really isn't much of a technical for the vast majority of them to do so. Most apps update automatically on their own these days, and users who personally own and use more than a Mac or two (the typical restraint applied by most traditional software licenses) are edge cases.
For those who really want to move to an all Mac App Store lifestyle, it might be best to wait for your favorite apps to get major upgrades in the store. With any luck, developers may hold a sale to celebrate the launch and entice non-App Store customers to buy in. Regardless, the purchase (well, 70 percent of it) will still go to a worthy cause--supporting the growing third-party Mac developer ecosystem.