There actually is a way to disable the remote control such that it can't lower the window. You'll need to find a Toyota dealer who understands what Customizable Body Electronics Settings, or C-BEST settings, are. My dealer doesn't get it.
The body electronics have a few settings that can be changed. Search the forum for "C-BEST" and you'll find the list.
These are the things where the Owners Manual says something like "this behavior can be changed - see your Toyota dealer for assistance." My dealer told me that the manual was wrong, and nothing can be changed. I know that's not true, since my last car was a Lexus, and Lexus has had C-BEST settings for many years (now called "Lexus Personalized Settings", or LPS). The Toyota vehicles use similar (if not the same) computers, and 4Runner has had some C-BEST settings since 2003.
The way to change C-BEST settings is for the dealer to plug in their OBD scan tool and go through the menus. To get to the Back Window setting, I believe this is the sequence:
"Application Select" Menu: Customize > New Vehicle > plug it in to OBD > Individual Change > Wireless D Lock > B Window Open
Choices for "B(ack) Window Open" are 1 TIME, 2 TIMES, 0.8 PR, OFF. Default is 0.8 PR, which means to press and hold the button for 0.8 seconds. To turn it off, select OFF.
After making the change, the tool asks "Are you sure?"; press YES to confirm, and it's done.
The dealer will most certainly charge you for the labor to do this.