By and large most medium merchants were sunk with one torpedo, and like as not they would stop fairly quickly. That said, there were many examples of merchants sailing away.
http://uboat.net/allies/merchants/ships/2966.html
http://uboat.net/allies/merchants/ships/2966.html
One thing the records show is that it was rare for a medium merchant to sink after just one torpedo. They usually took two or even three.
On the other hand there was this tanker whose crew abandoned ship after not being hit by a torpedo that detonated early. The u-boat kaleun then fired a second eel that ran deep and detonated on the far side of the target. Thinking he had sunk her he departed the area. The crew reboarded the ship and sailed away.
Three years later she was sunk by another u-boat.
http://uboat.net/allies/merchants/ships/2578.html
One American sub chased a Japanese freighter for six hours and hit it with eight torpedoes before it finally sank.
And of course there was
San Demetrio, which was shelled by
Admiral Scheer. The crew abandoned ship which then sailed away on its own, made a huge circle back to the crew, which reboarded her and finished the trip.
http://en.wikipedia.org/wiki/MV_San_Demetrio
You're right, most ships should stop after one torpedo, but it can also be argued that you shouldn't be surprised or cry foul when they don't.