The question is if you didn't bring that little boy back to life and saved the mayor instead, could you have lived with yourself? Would you have still been the same person?
We can't ever evaluate our actions based on what they lead to, because we have no way of knowing that when we make those decisions (most of the time). We can only evaluate our choices based on what we knew at the time.
Dr. Tenma, you're still a hero in my book, and I'm glad you saved Johan. The Monster Johan became/is isn't your fault.