The OS X app store will be optional. People who don't want to use it can still develop, or buy, apps the same way they do now. It won't be a replacement for the current way to buy apps; it will be in addition to.
Major, complex apps like Adobe Creative Suite or Microsoft Office will still be sold just the way they are now. Developers will still be free to sell apps off their own Web sites or on CD or DVD or whatever. The App Store does not control what you can do with your Mac; unlike with an iPad or iPhone, you will still be free to get apps in other ways if you want.