A couple of thoughts:
I'm not experienced with .NET 2.0, but it might be that there are options for embedding files from the command line compiler that aren't available in the IDE. Not very convenient, but the option may still be there.
If not, you still have lots of options within NH. The recommended method is adding all the mappings in an assembly using AddAssembly(), but NHibernate.Cfg.Configuration has about 10 other methods for loading hbm.xml from streams or files. Check out AddFile() and AddDirectory(), they should be able to help you if you can't embed a resource.
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