In real life, ship-fired torpedoes have a feature known as an arming run to prevent a torpedo from detonating too close to the firing craft (http://www.navweaps.com/Weapons/WTUS_WWII.php). The warhead of the torpedo is armed only after the torpedo has moved a preset distance away from the launching craft.
If I were a Wing Commander of a flight of X-wing fighters, assigning my pilots make precision attack runs against a small target, flying in single file formation within the confined close quarters of the equatorial trench of a space station, I would make sure that the explosion of a proton torpedo that missed would not adversely effect the spaceframe, targeting sensors, shields, or pilot eyesight of the next fighter on the attack run - allowing for maximum survivability of my fighter group and better odds of a successful mission. A successful proton torpedo would have to travel a long distance from the opening of the thermal exhaust port to the main reactor of the Death Star - it makes tactical sense to use the arming run of the torpedo to prevent the torpedo from detonating prematurely.
So, it is my theory that the proton torpedoes used in the assault on the Death Star were configured with an arming run, and at the time of impact on the surface of the Death Star, did not have armed warheads and the minimal damage sustained by the surface of the Death Star was only the result of the amount of kinetic energy the torpedoes transferred to the surface armor.