Hello Kirk, Craig,
I see exactly the same behaviour on my system (Mac 10.6.7, PM 4.6.7 latest beta). Which is weird because if PM where to treat symbolic links as any file, this should not happen; it should delete the symbolic link file, not the original.
(I have PM move deleted files to the trash, but this has no bearing on the problem; PM simply deletes the wrong file)
As a further note to this problem (I think I mentioned it before), PM does not support aliases at all either. A real pity as I would like to be able to have aliases/symbolic links to directories and files. This would allow me, for instance, to have my directories/files in one location on a drive, but also in another (a wish that may become less urgent when we the catalogue function is implemented).
Cheers,
Hayo