Like Paddle Guy, I have a Thule rack with the canoe brackets.  The under hood attachment points with some cordage are great ideas.  Thule and other suppliers actually sells some devices for use under hoods/trunks/rear hatches that can be temporary such as these   (You need to Login or Register or ones that you can bolt underhood thru a grommet and leave permanent and out of the way when not in use as suggested, like these   (You need to Login or Register .  They look easy enough to make on your own with a bit of craftiness and some handiwork, althought the price isn't out consideration, weighing the potential consequences. 

Nice thing about those aluminum canoes....you can always get some money back out of them from the recycler no matter how bent up they are!  ;D

pd