MCU getting powered up through GPIOs
Leave the MCU powered and put it into a sleep mode.  Much better practice. Also, you wouldn't need that regulator anymore.

Note that on many datasheets, "Absolute Maximum Values" are defined as relative to Vcc.  This isn't real meaningful when Vcc is floating (and meaningful in a bad way if Vcc is zero) -- so powering DIO pins when the microcontroller is off is just not great practice.