In the campaign:
If you cannot proceed, the failure music is played.
If you can proceed but some primary objectives are failed, the half-failure music is played.
If you can proceed and all primary objectives are satisfied, the success music is played.
-->Thus, for missions where there was a disaster but you can still proceed, the mission designer should make sure that some primary objective was failed. If you have a situation like where the Colossus was destroyed but the success music still plays, it's the fault of the mission designer.
I'm less sure about what happens in the single-mission simulator, but Phreak and I both added some stuff to make the proper music play. I'm not sure if we cancelled each other out, though. The incomplete objectives are supposed to be forced to false, but try failing them and see what happens.