The only U-boat I know to have been sunk deliberately by an Allied merchant ship was U-633, which was sunk by the SS Scorton on the 10th March 1943. U-633 was on her first war patrol at the time, and joined the wolfpacks attacking convoy SC121, running from Cape Breton Island to Liverpool. She claimed one ship from the convoy, but was rammed and sunk by the Scorton. It was originally thought she had been sunk three days earlier, by a British aircraft, but later research showed that this attack had actually been on another U-boat. Her profile on U-boat.net can be found at http://uboat.net/boats/u633.htm.

You might like to know the in both WWI and WWII, some merchant ships were equipped with naval guns which were hidden, these were known as Q-ships or Mystery Ships. Due to the tendency of U-boats to prefer to sink unescorted ships using their deck gun, (so as to not expend torpedoes which they usually had less of) as the U boat approached the merchant ship would reveal its gun and open fire on its unsuspecting opponent. The tended to be quite effective in WWI Sinking 14 and damaging 60 U-boats, however by WWII U-Boat tactics had changed and their torpedo capacity improved and the 9 British and 5 American Q-Ships were discontinued in 1943.