The NuGet packages doesn't specify a version constraint on them so they get the latest dependency, in this case v2.0.0.668. You could uninstall the current version of protobuf-net and just install the one that's needed, e.g:
PM> Uninstall-Package protobuf-net -Force
PM> Install-Package protobuf-net -Version 2.0.0.640
Otherwise another option is to add Binding Redirects in your web.config.
I'll look at specifying explicit versions for external NuGet dependencies in future.