President Obama justifies the civilian casualties of his drone program as collateral damage of war that is preferred to "conventional" military tactics. He explained that invasions and military tactics will cause more casualties and are less precise, thereby justifying the lesser evil of drones.
He further justified the drones as the course of action least likely to cause diplomatic tensions and civilian deaths. Any military action is risky, and this is the least risky of all the military counter-terrorist strategies.
Congress is briefed on every drone strike and was also aware of the strike on Anwar al-Awlaki, the American citizen who was a spiritual motivator in Yemen.