I'm strongly +1 on this one. I package Python RPMs for Fedora and I know what mess can come out of installing through both RPM and easy_install/pip.
In Fedora, both Perl and Ruby use vendor specific dirs for installing RPM packaged modules and site specific dirs for installation via cpan/rubygems. Since I'm also Ruby maintainer, I was able to watch how the confusion of Ruby developers disappeared after we introduced this approach in Fedora 17 (and rubygems stopped uninstalling RPM gems, which was always causing unsatisfied dependency problems). So I think Python should also go this way and provide a configuration option to use vendor-packages. Please note, that Debian packagers have been patching their Python package downstream for quite some time, introducing "dist-packages" into their installation. I think that they didn't experience any significant problems so far, which pretty much proves that this is feasible (and also their patches could probably serve as a base for patch for cPython).