As several of you have hinted but no one has precisely said it (and I'm not sure this answer is precise - it seems awful long to be precise)
:
Once the ball is hit (by the bat), the defense must be afforded opportunity to field the hit ball. If the runner interferes with this opportunity, then the runner shall be called out.
Once the defense has had their opportunity (muffed or deflected the ball), the runner is no longer in jeopardy if he is hit. His act would be unintentional if the deflected ball were to hit him - the defense caused the ball to hit him. You can't call a runner out for that; even if another defensive player were in a position to make a play. The runner was only hit because the ball was deflected into him by the defense. LIVE BALL. PLAY ON.
Now, the ball is deflected and dribbling toward the shortstop and the runner collides as the SS fields the ball. Umpire must make a judgement of the runner's intention. The SS
MUST go to the ball to make his fielding effort (even after it has been deflected). The runner, however, can run anywhere. Therefore, the greater responsibility for the collision, or avoidance of a collision, is upon the runner.
If the shortstop is capable of making a position adjustment to field the ball, the runner should also be capable of making a similar adjustment to avoid the collision. If the adjustment is not made by the runner and a collision occurs, I have intent and the runner is going to be called out.
Intent is not really that difficult. Was there opportunity for the runner to alter his course; did the runner make an effort to avoid the collision?
If the answer to the opportunity question is no, then there can be no intent to collide. Live ball; play on.
If the answer to the opportunity is yes and an effort was made, again, live ball, play on.
If the answer to the opportunity is yes but it seemed that no effort was made or that the runner created contact (hoping to disrupt the play) then I've got DEAD BALL, RUNNER IS OUT. And if the contact is egregious, I may have an ejection, and I would have no qualms calling another runner out if I felt there was defensive opportunity for a double play.
Seems pretty basic. See the big picture.