Very often I've had issues of apt and yum either uninstalling during an upgrade, or not working afterwards.
i'd be impressed if yum removed something that was not obsoleted during an upgrade. The code that follows out removal dep trees is never encountered during an upgrade request.
Now, I've never had either one mess anything up without telling me that it would (or least might) do so first, and making me confirm the action after that warning was issued. So, it's up to the user to protect themself from themself. ;)
-sv
-- Eric Rostetter