We have a custom board based on AT91Sam9g45-EKES and the designers connected the NAND Flash's WPn line to a pin on the MCU instead of just pulling it high.

My question to you, how would I go about hacking SAM-BA so that it pulls the PC9 line high when enabling NAND Flash?

Use TCL_Write_Int to poke arbitrary memory locations, specifically to enable to PIO, pin directions an state. Recompiling the applets is probably more fun than you want.

You could look at how other TCL scripts to this, but here's a rough example :

# Reinitialize AIC
TCL_Write_Int $target(handle) 0xFFFFFFFF $AT91C_AIC_IDCR dummy_err
TCL_Write_Int $target(handle) 0x0 $AT91C_AIC_SVR dummy_err
# Clear AIC source
TCL_Write_Int $target(handle) $AT91C_ID_PIOC $AT91C_AIC_ICCR dummy_err
# Clear current IT on PIOC
# Acknowledge the IT with PIO_ISR
TCL_Read_Int $target(handle) $AT91C_PIOC_ISR dummy_err
# Disable IT DRXD on PIOC
TCL_Write_Int $target(handle) $AT91C_PC16_DRXD $AT91C_PIOC_IDR dummy_err