The actions taken by the Japanese in the aftermath of the Doolittle Raid were specifically against those parts of China where they knew the Americans would have had to land the bombers (or bail out of them); the Japanese actions here were done purely out of retaliation against the Chinese for their (presumed) assistance to the American airmen.
That the Japanese were barbaric to the Chinese before and after the Doolittle Raid is, I think, obvious to us all. But if you're suggesting that the Japanese military would have mobilized a week after the Doolittle Raid and gone on a tear for a month to destroy some 20,000 square miles of China and murder an estimated 250,000 people over something else, I don't buy it.
This was the price paid for the Doolittle Raid; while we may not have intended it, we stuck an ally with the bill.
Would they have done it at some point?
Absolutely.
It was sort of like the Warsaw uprising. Did the Nazi's kill everyone involved they could get their hands on? Yes. Were they planning on killing them at some point anyway? Yep.
You would be on far firmer ground in the case of Reinhard Heydrich's assassination as the Czechs were not slated for whole scale extermination in any case.