I don't do much... no: *any* C++/CLI - but I guess the conflict here is that the c++ generated classes are not going to be CLI-friendly. So you need to either use a c++ library and c++ classes, or a managed library and managed classes.
If your framework is unmanaged c++, then I *suspect* your best bet might be to accept managed types, and then map them manually to the unmanaged types, before feeding the unmanaged types to the unmanaged library. However, to your question about using the generated C# files in a C++/CLI project: yes, that will work - but you'll have to use a matching managed library - so if you use protobuf-net generated types, you'll have to use protobuf-net to serialize/deserialize. And likewise with protobuf-csharp-port generated types and the protobuf-csharp-port library.
I'm not sure if I added anything there, but...
Marc