Respectfully, I don't see how putting the assemblies on NuGet "will only make this worse".
People "create version inconsistencies" by upgrading NCrunch to the next version, NOT by referencing a new Framework version. The framework version is only going to be updated when the NEW version of NCrunch stops working with the OLD Framework DLL. If you are trying to prevent inconsistencies altogether, the *only way* to do so is to stop releasing new versions.
If it were me, I would trust people to be able to keep NuGet packages in sync much more than I would trust them to manually manage DLLs by extracting them from the GAC.