It doesn't allow fighting. Fighting is a penalty. Do you also consider boarding and hitting from behind to be 'allowed'? Fighting is just allowed in the sense you don't get kicked out of the game (at the NHL level). But what's your point? Are you going to suggest a player shouldn't punch someone in the face because baseball doesn't allow it? Turns out they don't allow you to purposely bean someone either.
Football is also a high contact sport and they don't need to "allow" fighting so players can 'police the game themselves' - in fact there's very little if any retaliation after unsportsmanlike celebrations (their version of a bat flip), chop blocks, helmet to helmet hits, low hits (or even just massive hits) on the QB.
I just think throwing a baseball at someone is a pussy move. I've done it several times over the years and after the adrenaline wears off, I always reflect and think - f*** what a pussy move that was. It didn't change or solve anything.