If the use of a nuclear weapon against Japan was morally and militarily justified (it saved Allied lives,and,less important, Japanese lives) why would the use of a nuclear weapon against ISIS not be justified morally and militarily ? It would also save Allied lives,and,less important, Muslim lives .
I don't think it wise to view peoples lives as more or lesser important. This sounds like Nazi ideology.
Certainly the US wasn't as concerned about collateral damage in WW2 (again different situation altogether) and the fact that is that Imperil Japan murdered 10 million innocents. However it did end the war.
Again one cannot compare WW2 with the current ME situations. If an atomic bomb is used in the ME it will open up a can of worms. It will galvanize the radicals against the say US or whoever else that uses the A-bomb.