Base Award Question

[Fan10]

Saw an odd play yesterday: In an NCAA D1 game with runners at 1B and 3B, the offense tried the double steal. As the catcher threw down to 2B, the runner at 3B broke for home. The second baseman caught the ball as the runner from 1B pulled up short of 2B. Then, the second baseman tried to fire home and threw it directly into the pitcher's back. The ball bounced all the way into the dugout.

Of course, the lead runner was awarded home. Initially, the other runner was awarded 3B, but after a conference between the umps, he was awarded home. The defensive coach came out for an explanation, but after a brief discussion, he was fine with it and went back to the dugout.

I know that I must be missing something (especially considering the defensive coach was fine with it), but does anyone know why he may have been awarded home?