What is the proper ruling on this?

[ump66]

Runner on third base and batter walks on ball four. As he is trotting to first, the defensive coach begins walking to the mound and asks the PU for time. PU says, "you can't have time until the BR reaches first". Well, BR gets to first and coach is already over the chalk line and in the infield grass and BR runs right past first and heads for second. Defense lets him go to second to prevent runner on third from scoring. Coach and PU get in heated discussion about why he wasn't granted time, and in the end, PU puts BR back at first. I was wondering what your thoughts were on this. I can see why he did that if he said to the coach, "you can have time coach once he reaches first base", but he can't assume the play will end at first! Needless to say the offensive coach didn't appreciate the call.