Ok. Optimal outcome. Assuming they did not do a complete wipe out of our intellectual and tactical minds and that their main fleet is not present, we should theoretically be able to infiltrate, sabotage and employ industrial and political espionage and eventually overthrow their rule. Whatever was left of their population should be allowed to stay and assimilate however notified that if they make a false move they will be made an example. We should then proceed to learn even more about them,in-depth study (by peaceful means) of social and political order, biology, technology, military tactics. All that assuming their FTL drives are not advanced enough to make the journey in less than...say five years. Then open up comm-channels, set our conditions for at least neutral co-existence. Should they fail to comply, we will make clear that when given the chance (which we have had) we are a military force to be reckoned with. Then proceed to decimate their forces but leaving the civilization as intact as possible.
However, knowing what us humans are like, we will most likely get all the knowledge by force and proceed with remorseless annihilation.
Worst possible scenario, as some have pointed out, orbital bombardment, persecutions on surface after uprising attempts and eventual extinction of our species