Would it be possible for Winterboard to make it so when you go to wiggle mode it shows the little uninstall X on the jailbreak apps? And when you tap it, it could show a pop up that is the same as the AppStore apps, and then when you hit Delete it could issue the command:
apt-get remove package.indentifier.whatever
Seems like it would work to me. The only problem is that it'd have to ask for the root password, but that's fine with me because when you install programs it asks for your iTunes password.
Or maybe it wouldn't. How does Cydia install programs without the root password?
apt-get remove package.indentifier.whatever