... I could manually change the filename field for the songs I don't want to keep to point to the one I do want to keep, and manually delete the rest. Not pretty, but wouldn't that work?!
No. One disk file can exist only in one MC Album. You can make your own tags for the other album names, but MC don't handle them as separate albums. The only way to keep them together is to do a playlist for them.
Currently it is possible to have one huge APE file for the whole Album (one CD disk). Monkeys Audio can do APL files for linking a certain position of that APE file to a logical track. An APL file includes also tag information for an individual track. APL files can be imported to MC and used as regular audio files. It is possible to make a copy of an APL file and change e.g. the album tag and keep both in the library.
What we need now is a similar system for individual tracks. A sort of Media Center link file (could be named as .mcl). That would include tag information and a link to the main file. It should support all audio formats. The mechanism to make them could be in Convert Format (of course "Send original files to recycle bin" should be disabled).
There is already support for the APL files. Perhaps just a slight modification is needed.