If you don't want to wait for an update, there's an easy fix. First install and open up iFile from Cydia.
Navigate to /var/mobile/Applications/, tap the gear in the bottom-left corner and make sure 'Application Names' is set to On, and then find the app you want to update and/or buy inside that folder. In the app's folder, there will be a file called iTunesMetadata.plist; delete it. Now go to the App Store.
Search for the app, and you'll notice that the App Store thinks it's not installed on your device. Click the 'Buy App' button and purchase the app. It won't overwrite any of your saved data from the app, and you'll have legally purchased it. This will also work for any apps that you want to reinstall without losing their saved data.