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I found the cause of the behavior (perhaps it is common knowledge, but I am new to python source); imp.load_dynamic calls the following functions
 Python/import.c: imp_load_dynamic (http://hg.python.org/cpython/file/ad51ed93377c/Python/import.c#l1777)
 Python/importdl.c: _PyImport_LoadDynamicModule (http://hg.python.org/cpython/file/ad51ed93377c/Python/importdl.c#l23)
 Python/import.c: _PyImport_FindExtensionObject (http://hg.python.org/cpython/file/ad51ed93377c/Python/import.c#l525)
where the last one uses the extensions object (http://hg.python.org/cpython/file/ad51ed93377c/Python/import.c#l32), which is explained at http://hg.python.org/cpython/file/ad51ed93377c/Python/import.c#l449
 Magic for extension modules (built-in as well as dynamically
 loaded). To prevent initializing an extension module more than
 once, we keep a static dictionary 'extensions' keyed by module name
 (for built-in modules) or by filename (for dynamically loaded
 modules), containing these modules. A copy of the module's
 dictionary is stored by calling _PyImport_FixupExtensionObject()
 immediately after the module initialization function succeeds. A
 copy can be retrieved from there by calling
 _PyImport_FindExtensionObject().
The fact that extensions are keyed by file name explains why opening the .so through symlink does not return the old extension object:
 # foo.so
 # bar.so -> foo.so (works for both symlinks and hardlinks)
 imp.load_dynamic("foo","foo.so")
 imp.load_dynamic("bar","bar.so") # will return the bar module
I will investigate whether marking the module as capable of multiple initialization could be a workaround for the issue -- since the quoted comment further says (http://hg.python.org/cpython/file/ad51ed93377c/Python/import.c#l459):
 Modules which do support multiple initialization set their m_size
 field to a non-negative number (indicating the size of the
 module-specific state). They are still recorded in the extensions
 dictionary, to avoid loading shared libraries twice.
To fix the issue, I suggest that the *extensions* dict is keyed by (filename,modulename) tuple for dynamically loaded modules. This would avoid any ambiguity. Grepping through the code shows that the *extensions* object is only accessed from Python/import.c, therefore regressions should be unlikely. What do you think?