Brian,
First let me address your hypothetical play.
So, a ground ball up the middle is misplayed by the pitcher and get's redirected toward the second baseman only to be unintentionally kicked by the runner going from first to second while the second basman is attempting to make a play on the ball and the runner is not out?"
In your example, we have a batted ball that is deflected. Generally, a runner is protected from interference when hit with a deflected batted ball. The ASA rule is 8-8-F.
"A runner is not out...when hit by a fair batted ball after it touches, or is touched by, any fielder, including the pitcher, and the runner could not avoid contact with the ball."
On your play, we have a batted ball that was deflected by a fielder and the contact was, as you said, unintentional. The runner is not out and the ball remains live and in play. The umpire must judge if the deflected ball was avoidable or not. If it was, then the runner would be out for interference.
I would apply this same principle to the dropped third strike play. If the catcher deflects the ball into the batter-runners path, making contact with the ball unavoidable, I would have the B/R protected from interference.
If the kick of the ball is judged to be avoidable or intentional the B/R would, of course, be out.