Jon shot Otis to create a decoy for the advancing zombies, man.
This guy's actions have painted him as a man with VERY questionable character. Think about it. He almost rapes dude's wife at the CDC; he puts a bead on Rick out in the forest; he leaves him at the hospital; he moves quick on Lori when he "thinks" his friend is dead; he shoots Otis ... he is unstable, at best.
I love this show. Great dialogue and acting. And the zombies are wonderfully made up.