How can I programatically log another user out in D7?
drupal_session_destroy_uid() sounds like a safe bet:


  Ends a specific user's session(s).


The core implementation clears the database, as you'd expect, but any module that overrides session.inc, and doesn't provide a working implementation of that function, would surely be considered broken (as user_delete_multiple() and other functions need it).

So in theory you should be able to use that function regardless of the storage.