I am not sure how hot MDDs normally run but have you made sure the fan you installed was pointing in the correct direction for the MDD case?(and not just the same direction as the previous aftermarket fan was installed) Also, have you checked any other fans to ensure someone did not screw around with them as well?(again, IDK how many fans a MD actually has)

At the end of the day though most of Apple's cases are not really known for good airflow.

To test your heatsink theory you could close the case and rest the whole thing on it's side, but unless someone altered the mounting hardware it is probably fine. You would be surprised what you can hang sideways!