There are times when I have a component in an assembly and I realize that component should have been an assembly instead. This most often happens when I need to add pins to the part or something small like that. Starting with Wildfire 5 there was an enhancement made so that if a part is duplicated it could be replaced using the unrelated component and evaluation rules.
I would suggest that these rules be updated to look for a component within an assembly. If the component being replaced exists within the assembly that you are replacing the component with, the entity IDs should be able to be auto paired.