It's not perfect, but what I've started trying is replacing the 'Filename' tag in the properties of the two duplicate songs to point to the same physical file. This way the MC database thinks there are two songs, even though there is only one file. What you have to do is rename/delete the file you don't want (otherwise if MC can still see it, it tries to overwrite the other file when you change the filename), go into properties, and under the 'File Info' subset of 'File Info', there's a field for 'Filename'. Pretty straightforward.
The main problems with this that I can see right now are that if you update the tags from the library, it'll update the tag twice with different information. And if you use the update library from tags function, it'll screw up one of the library entries. Just in case, I've backed up my library.