If the AVR causes a pop to come through the speakers and the trigger has been assigned to Zone On, you could assign the 'Trigger Off' function to an unused input but I would assign it to all of the inputs you use- it won't turn off when you switch from one input to another. If it has been assigned in order to switch the power for an amp that's used for Zone 2, I would do the same- assign Trigger Off to an unused input. Then, add a 1 second delay before shutting down the rest of the system.
If the amp doesn't thump when you shut the AVR off, I wouldn't worry about delays or sequencing, but by using the word 'sequence', I assume you're using a Harmony remote. If so, which one?