When it comes to prosecuting on field incidents, charging a player with a crime can get tricky. If we head down this road, you could see a player who gets hurt in the course of a game file a lawsuit against the opposing player, citing loss of income, livelihood, etc. Should a player get suspended for a Flagrant-2 foul? In most cases, yes. Should he get sued or charged with a crime for it? I don't think so.
However, anything involving a non-competitor (referee, coach, especially fans) I think there is a definite need for a criminal investigation. Once you are out of the scope of the field of play, that changes everything.
I think the player who threw the ball into the stands last night should definitely be charged. It was a premeditated act and he knew he could have injured someone. While it is a fan's responsibility to watch out for foul balls, broken bats, etc. they should not have to attend a game wondering "Gee, I hope a player doesn't throw a ball as hard as he can into the stands tonight!" That is out of the usual scope of gameplay. Then again, I'm not a lawyer so I have no idea what legal recourse could occur here.
Anyway, I am squarely in the "if it happens during the game, it probably shouldn't be a crime" boat, because of the bad precedent legal actions could set.