Actually, I agree. They never enforced that rule and picked an odd time to start. It was a head's up play by Evers, who knew the rulebook. It's losing on a technicality.
I recently read The Celebrant
, which is a fictional novel about Christy Mathewson, but the baseball elements are unaltered, according to the author.
Apparently three weeks earlier, Evers tried this shite on the Pirates (exact same situation with runners on the corners in the bottom of the ninth), but the umpire O'Day did not believe Evers in that game, so he did not call the runner out.
However, this incident led O'Day to keep an eye on Evers and to make sure the runner touched the base. Sure enough, O'Day clearly saw that Merkle made a dead sprint to the clubhouse to avoid being crushed by the fans.