I don't have the quotes on me, but Ender eventually figured out that the Formics - **intentionally** - pulled all of their queens (aside from the designated successor on what would become Sheakspeare colony) to their home planet. Basically, the committed "[suicide by Ender][1]".

I don't recall any mention of IF knowing this at all. They just wanted to wipe out as many Buggers as they could (if you defeat the star fleet defending a colony, you can then take over, the fact that the Buggers all died when their Queens did was just a cherry on the cake).


  [1]: http://en.wikipedia.org/wiki/Suicide_by_cop