I suppose you'd prefer that, instead, the entirety of Japan would have had to be bombed into oblivion using non-nuclear weapons, not to mention the extra loss of life on the Allied side that would have almost certainly occurred during a more traditional invasion that would have likely been necessary.

War sucks, and there are rarely good choices; it's nearly always going to be a choice between something truly awful and something just merely really bad. Nuclear weapons suck, but I dare say they saved lives -- on both sides -- when used in that instance. Of course, after more people had them, and we realized the implications of MAD, using nuclear weapons is (thankfully) more or less off the table for any non-suicidal nation.

There were other options besides just those two. Japan at the time would have accepted any peace agreement with just a single clause: that the Emperor would not be executed. Anyone else could be. This was a reasonable agreement to make since the US didn't execute him anyway. The war could have ended in the same state that it ultimately did with far less loss of life on both sides except for the US insistence on unconditional surrender.