I made some untested mod packages for the Far Cry Mod Installer that should disable controller support for various Far Cry games.
These mods are based on the mod macntrash420 made for Far Cry 2.
P.S. For Far Cry 6, it seems like its original actionmaps\hid_definitions.xml file contains some definitions for supported controllers. Maybe you can figure out your own controller's Vendor ID and Prod ID from Device Manager, and add support to the xml file. If you want to do that, simply open the FC6_Disable_Gamepad_controller_support.a3 mod package file in a Zipfile editor (like 7Zip), and update the file with your edits there. Then, save the package & install it with the Mod Installer again.