The Dukes rolled up 602 yards offensively, 377 on the ground.
After Dae'Quan Scott opened the scoring on a 1-yard run with 9:18 elapsed, Thorpe rushed 15 yards for a TD late in the first quarter.
The senior quarterback scored twice more in the next 8 minutes, first on a 9-yard run with 12:16 left in the half, then with a 41-yard scoring strike to Scott.
Thorpe was 15 of 27 for 177 passing yards and had 76 yards rushing.
James Madison led 34-0 at halftime in the first meeting between the two programs.
Trailing 41-0, St. Francis got on the scoreboard when John Kelly threw a 2-yard scoring pass to Kevin Parker to cap a 13-play, 75-yard drive.