Offensive indifference is not always considered as intentional (how many times does an offensively indifferent R1 get plunked in the back when F3 throws to second trying for the out.) and should not be treated as such (and any documented interp that says otherwise, needs to find file 13). You have a whole series of things to think about before you can rule properly.
1. Did the runner show intent to interfere.. if yes, out.. no more thinking needed... If not, continue
2. Was the runner doing as they were supposed to? This one is a bit more detailed, but if the runner is in the act of crossing home plate, you have nothing.. if the runner is just standing there, you may have something. If the runner has crossed but is in the act of stopping his/her momentum, you probably have nothing.
3. When the runner started for the dugout, was the ball still rattling about the backstop? Anotherwards, did the runner have any idea where a possible throwing lane may occur. If the answer to this is yes, the offensive indeference comes into play, where the ex-runner should have paid attention... if the answer is no, the catcher had to stop the ball, the runner was trying to guess. I would not call this one as the runner is trying to get in the clear.
4. Was there intent on F2 to hit the runner with the ball? If yes, you have nothing (and the players will think of and try this when you least expect it, trying to entice an INT call.)
In short, there is no short answer here. It is pure judgement on the calling umpires part as to how to rule. As a TD, I would not touch this one as a judgement call that cannot be protested.