Brad,
Do you use a keyway or rebar dowels to tie the wall to the footer? I would think that it would be difficult to install a membrane between the footer and wall if there is a keyway or dowels in the way. There might be a spray on membrane that you could use.
The code official in my area allowed us to install a waterproofing membrane under and beside the footer. Would this work for you also? With this method there was nothing in the way to work around.