lsusb shows us that—sure enough—Apple's IR receiver is being loaded on boot:

# lsusb
Bus 005 Device 002: ID 05ac:8242 Apple, Inc. Built-in IR Receiver

lsmod reveals hid_appleir is the module being loading for our remote. Let's blacklist it:

# echo 'blacklist hid_appleir' > /etc/modprobe.d/hid_appleir.conf
# depmod -ae
# update-initramfs -u
# reboot now

That should take care of it!

More helpful tips and explanation here: https://wiki.debian.org/KernelModuleBlacklisting