Use GPIO for switchable Pullups of I2C
Your use of a GPIO pin to pullup the the I2C bus resistor is a reasonable idea as long as the MCU in use has GPIOs that have a strong active high level output. 

You will need to use two GPIOs, one for each resistor. If not then the two resistors are going to put 2x 4.7K ohms between the two signal lines.

So you have a tradeoff. Use two GPIOs for this or  one GPIO and two small switch FETs. Or you could equip each resistor with a two pin header and a jumper and use no GPIOs at all.