For most objects, you can set the 'Store transformation' setting in the preferences under 'Behavior → Transforms' to 'Optimized' to make Inkscape manipulate them directly instead of adding transform attributes whenever possible. There is also the 'Apply Transforms' extension to remove already existing transforms while keeping the object at the current position.
<use>-elements however, it seems like the developers have decided to always use transforms on clones instead of using their x and y attributes (at least I have never seen them set to anything other than '0' by Inkscape). You'll have to manually set these values with the 'Edit → XML-Editor...' afterwards (the 'Apply Transforms' extension doesn't seem to work well with clones either).
It probably wouldn't be that hard to write a script to do this automatically, though. Especially if the transforms only have