If Torque is within 3 squares of the enemy, then after the initial frag routine he checks again to see whether the enemy is still there, and if it is then he launches another missile to finish it off.

The re_check: routine performs this check. If no enemy is found, then Torque returns to his normal hunting routines. You probably realise that there is a chance of getting the flag from the dead enemy. However, Shea has not implemented this. I presume that it might be quite difficult to get around the obstruction to the flag, if it is anything other that a single barrier. Also, a long flag-finding sequence would leave Torque vulnerable to attack.