Your debian/rules install target must never install any files outside of the build tree. Instead, it should be installing to the package build directory (which, depending on how you're building the rest of the package, is probably debian/$packagename/
. With a setup.py, the right switch to accomplish this is --root=debian/$packagename
.
If you use dh_python2, dh_auto_install, and other debhelper tools appropriately, they will take care of that for you, plus a lot of other important housekeeping such as bytecompiling for various python installations on package install.