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I had the same issue on Indigo. I was able to resolve it without uninstalling ROS by using dpkg to remove the problem packages without removing their dependencies.
dpkg -r --force-depends package_name
So I ran the following:
dpkg -r --force-depends python-pyassimp assimp-*
This removed the problem packages, I then removed Cuda and ran apt-get -f install
which reinstalled assimp with the correct version for indigo. I've been using it successfully since then without errors.