I don't think so. It's my understanding that your app has to be WinRT/Metro app to be installed & updated via the app store. At best Microsoft will allow you to promote your non-WinRT/Metro app by providing you a means to list your app in the store but the listing will be nothing more than a re-direct to your web site where they can purchase the app.
I think it's pretty clear that it's go WinRT/Metro or go home. Despite Microsoft's allusions to the desktop being a viable option for developing apps they are killing it with a thousand little cuts with moves like this. I just wish they'd come out and say it: their investment in desktop technologies is over. The desktop is your backwards compatibility box and that's about it.
I love this double-speak too:
Lastly but not the least, I want to address the feedback from users who would like WU to update their 3rd-party applications. People clearly find the experience with multiple updaters on the system less than optimal (and we agree!).... However, as we discussed at the //build/ conference, the new Windows Store will provide a one-stop shop for (free and paid-for) Metro style apps, with an integrated update service to help ensure apps are maintained in a consistent manner
Summary: We know having multiple 3rd party app installers suck. Instead of addressing the problem we'll leverage our app store to try and get developers to write Metro apps in order to take advantage of the apps store's update services.