check swing appeal - what a mess......

[newump]

1-2 count. no one on base. next pitch is a curve ball in the dirt. Batter takes a half swing. ump says "ball, no he didn't" ball rolls away from catcher towards the backstop. BR pauses for a split second and then upon seeing the ball rolling away takes off for 1st. no request for help is made by the defense. catcher quickly retrieves the ball, but BR is already standing on first w/o a throw. PU then beckons BR back to the box as the pitch was ruled a ball and now the count is 2-2. BR comes back to the box. then the defense team requests that PU get help. PU askes U1 if the batter swung at the pitch. U1 rules that he did swing. Catcher then throws the ball down to first. U1 gives an out signal. BR is still at the home plate area. Umps then send BR back to first as he had already reached first safely and was then put in jeopardy when he was brought back to the box by PU.

this was ncaa D1 conference game.

1. PU should have immediately asked for help if he thought it was close.
2. U1 should have offered his help immediately without waiting for an appeal.
if he thought the batter swung.
3. U1 should have said no swing once they reached that point (regardless of what he thought - just to avoid this mess)
but these things did not happen.
what would you guys have done?? could you call BR out ? would you not allow the appeal at that late time?? or did they do the right thing once they were faced with this scenerio
thoughts??