Greymule,

Mike is correct. On catcher's obstruction, manager always has the option of taking the result of the play or the penalty for catcher's obstruction.

So, in your example, if manager elects result of play, run counts and batter has a strike called on her. If manager elects the penalty, then runner is returned to 3B (unless they were forced to advance) and the batter is awarded 1B. Right Mike?