Not sure if that is a good solution since (a) you are making it more complicated by adding an extra step to move the folder and (b) if you move the folder, it can't merge them (this only occurs with the sort into subfolder action). I think the better solution is to enable Spotlight for the folder on your Time Capsule.
If you insist on going this route, I think you'd need to have separate rules to go into every folder and find the files and then move them, then sort into subfolders at the destination, using the "source folder" attribute. You'd also need to add a rule to remove empty folders.