If an interrupt occurs during a flash erase / program operation, the read while write restriction will be violated if the interrupt service routine code is located in the same flash block as the erase operation is occurring on. so you can disable / enable interrupts before / after the flash command operation. If interrupts are disabled, any interrupt that occurs during the flash operation will be pending when interrupts are re-enabled.
I would suggest you refer to the AN4695, this application note discuss important considerations and guidelines for implementing in-software flash programming on Kinetis and Coldfire.