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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.