The way i look at this is that he was not at all creating any threat anymore and killing him was always only going to prompt further terrorism and outrage. However letting him live would have looked cowardly and also after looking for him for this many years you would think that once they finally did find him they were not just going to let him walk of freely. He was a dead man walking.
Another point about this whole thing is that obviously with something on this scale and with a government as corrupt as the USA, there is obviously going to be conspiracies as to what really happened, some of these are things such as "why did he get sent out to sea so quickly after his death when only just the other day we had Gaddafi's son die and there was pictures of the body." Conspiracies will always exist and until proven correct (which with the amount of corruption in the government, is highly unlikely.) will remain as just theories.
Let us know what your ideas on this are :) !