AFTER LANDING AT PIERRE, SD, 2070 LBS OF CARGO WAS OFF-LOADED FROM THE AFT SECTION OF THE AFT & A NEW WT & BALANCE WAS CALCULATED. THE AIRCREW THEN PREPARED TO TAKEOFF IN CONDITIONS OF LOW CEILING & FOG. THE PLT-IN-COMMAND (PIC) INITIATED THE TAKEOFF ROLL, THEN AT ABOUT 80 KTS, THE COPILOT ASSUMED CONTROL AS PREBRIEFED. THE TAKEOFF WAS REPORTED AS NORMAL UNTIL THE FLAPS WERE RETRACTED. AT ABOUT THAT TIME, THE COPILOT SAW RED LIGHTS AHEAD. HE ASSUMED THE LIGHTS WERE ON RADIO ANTENNA TOWERS & PULLED BACK ON THE YOKE WHILE BANKING RIGHT TO MISS THE OBJECTS. THE RED LIGHTS WERE ACTUALLY ON SMALL STRUCTURES (SHED & LIGHTING SYSTEMS) AT THE NORTH END OF RWY 31. WHILE TAKING EVASIVE ACTION, THE RIGHT WING DUG INTO THE SOFT GROUND & THE PLANE CRASHED. WITNESS SAID THE ACFT WAS IN A SHALLOW CLIMB AFTER LIFT-OFF. ONE WITNESS SAID IT CLIMBED TO ABOUT 100 FT, THEN APPEAR TO LOSE ALT. THE ELEVATOR TRIM SURFACES WERE FOUND IN THE 1 TO 2 DEG UP-TRIM POSITION. ACCORDING TO PROCEDURES, THE FLAPS SHOULD NOT HAVE BEEN RETRACTED UNTIL ABOVE 400 FT AGL.