Do those charge pumps use external capacitors? If so, you could disconnect/float those capacitors, or if that would damage or glitch the chip, you could replace the real capacitors with some circuit like a voltage regulator + diode that would be designed to provide the charge pump output rail with a voltage that's high enough not to glitch the chip but low enough to be unsuccessful in writing to the flash. Would one of those ideas work, and allow the retrofit you envision to be designed with existing flash memory silicon + a few additional components?