Man, that's a tough call to make. However, here's the relevant portion of Rule 7.13:
Unless the catcher is in possession of the ball, the catcher cannot block the pathway of the runner as he is attempting to score. If, in the judgment of the Umpire, the catcher, without possession of the ball, blocks the pathway of the runner, the Umpire shall call or signal the runner safe.
Based on my parsing of that passage, overturning the call was correct. That said, I sympathize with Robin Ventura's very obvious frustration. The problem is not with how the rule was applied in this instance. Rather, the problem is that the rule is too broad, has no allowance for context and thus lends itself to inconsistent interpretation.
Q: It happened so quickly. Would you have had time to react differently if you knew the rule?
A: No because I know the basic premise of the rule and I don't think I could have done anything differently. That's such a short amount of time. If you put the whole play together. If it's a fastball away and the guy barrels it up straight to Jose, I see the guy's coming, that's different. This is a jam-job, broken bat flying by my head. The hitter is looking back where the bat is going. I realize the ball is in play over there. He's coming home. ‘Ok, I've gotta move up five feet to get into position to make a tag.' And like I said, this is all in a matter of two seconds. That's a lot to ask of anybody to have all those things go through your head in addition to catching a ball and making a tag. There's not enough time to be on top of every aspect of that play.
My thoughts on the faux "old school" credentials of plate collisions notwithstanding, I'm not sure this rule, as written, is properly addressing the issue.
If nothing else, though, this led to a vintage-issue "manager kicking dirt on home plate" tantrum, so in that sense it was worth it.