I think TM do the things fine, as it simple and powerful renaming files in the file drawer. That function has been for me really a time-saver and is very natural that it was there as is. The solution to the problem, IMHO, is to add a more complete behaviour to TM, allowing Option-Drag of files in the drawer. Also, perhaps, info for files (to make them executable, for example, via a dialog... although I think this is not so important...)