Hello Dave:
Actually the main issue is the EzPort mode, not the NMI handler. If the pin detects a low level at Power ON, then it will enter EzPort mode, so it won't even get to trigger the NMI interrupt. It would be better if you desolder the capacitor.
EzPort can also disabled. If you are using KSDK, then the Flash configuration registers are not handled by Processor Expert. In the first discussion I linked you can see there is a file called startup_MK64F12.S which contains the Flash Configuration:
/* Flash Configuration */
.section .FlashConfig, "a"
.long 0xFFFFFFFF
.long 0xFFFFFFFF
.long 0xFFFFFFFF
.long 0xFFFFFFFE
Change it to this to disable EzPort and NMI (see the F9):
/* Flash Configuration */
.section .FlashConfig, "a"
.long 0xFFFFFFFF
.long 0xFFFFFFFF
.long 0xFFFFFFFF
.long 0xFFFFF9FE
Regards!
Jorge Gonzalez