What is interesting is that even though the 2bman made the out by stepping on the bag, the only reason he would be given an error in real life, would be if a runner(s) advanced on the play. In your example, the runner at third advanced home, so that constitutes the error given.
Oddly enough, let's say the ball bounced off the dugout fence, and didn't allow the runner at third to come home, or the guy at first to advance to second, no error is given on the play.
The game has definitely had a hard time with what is an error or what is not, because there are some arbitrary and judgement calls as to what constitutes "normal effort" and therefore, the game will never get the calls 100% correct.
In the same scenario you gave us, had the slow runner at third held the bag, but a fast runner headed to first, made the turn and took second, it still is an error, as a "physical mistake" allowed the offense to gain an advantage (advancing a base).
I've battled it out with official scorers in my day, and I am still under the impression that errors were sometimes doled out based on their mood... Sometimes official scorers wake up on the wrong side of the bed too...
~syf