Half-Life remake Black Mesa has a Beta for a big update with a new UI and controller support
(www.gamingonlinux.com)
Just don't use the controller then. Everyone is aware that not everyone wants to play first person shooters with a controller. That's why its an option. This is a single player gamer where you can play as you wish, without affecting others. So what's the problem? Developers give more option, that is the opposite of awful.
I personally play some FPS with game controller, especially single player ones. And since the Steam Deck and Steam Controller playing around with gyro and trackpads is super fun.