So I have a raspberry pi connected to an array of 18 AVR microcontrollers through one of adafruit's I2C-friendly level shifters.

The ATMega328 datasheet is very clear in mentioning that a powered-off microcontroller will render an attached I2C bus inoperable. I'm fine with this (there are no other devices on the bus anyway), the problem is that when they are powered off (with grounds still connected together, and the level shifter powered on), the Pi gets stuck in the boot process at the point where the I2C driver would normally load.