These hypothetical questions are interesting. If Atticus had his way, then either Jem or Boo would have been charged. If Jem was charged, no charges would stick. Jem is a boy and Bob Ewell is a man. The court would have found Jem innocent and Bob guilty without a shadow of doubt. Jem would have been a hero.
If Boo were charged, things would have turned out very differently and badly for Boo. Boo would have not been charged, because it is clear that Bob Ewell was the aggressor, but Boo would have been put in the light of people's scrutiny. This would cause Boo great difficulty, because he is a recluse. He has been a recluse for so long that he does not know how to interact with people. Even if people saw Boo as a hero, it would not be good for him, because he does not want attention, good or bad. Therefore, the decision that was made at the end of the novel was wise.