Got it. To disable SWD on the fixed pins, and enable GPIO on those pins, instead, I created this function and call it before BOARD_InitBootPins().
Note, however, after you do this, SWD will not work as expected until you enable ISP mode. To do that, connect pin 4 (PIO0_12) to ground, then touch pin 5 to ground and disconnect. SWD should work again.
// near the other #includes
#include "fsl_swm.h"
// somewhere in your source code
void disableSWD ()
{
CLOCK_EnableClock( kCLOCK_Swm );
SWM_SetFixedPinSelect( SWM0, kSWM_SWCLK, false );
SWM_SetFixedPinSelect( SWM0, kSWM_SWDIO, false );
CLOCK_DisableClock( kCLOCK_Swm );
}