[AtlUmpSteve]

While it is true that the catcher impeded the runner from advancing, that isn't obstruction by a defender that has possession of the ball.

While whatever rulebook being used in that game may not define defensive flagrant or malicious contact, I seriously doubt any definition specifically excludes it. In the past few years (2007, I believe), NFHS Softball (at least) clarified in an editorial change that malicious contact could and should be applied to defensive players, not just offensive players.