Don't get me wrong, I love their games (when they bother to make one) and my Steam Deck. But lets not pretend that Valve is our friend either and their main goal is anything but to make money.
While I think that going so far as to delete my Steam library is a fairly extreme situation, I do think supporting a diverse marketplace and actually using other stores is a good idea. I have games on Xbox App (on PC), GOG, Epic, EA, etc. It really isn't that big of a deal to have alternatives installed, and if you are worried about the software there are alternatives like Heroic Launcher.
The controller situation is an interesting one though that I will need to do my own reading on, I knew that Steam tried to manage controller settings itself (which just further encourages you to only use Steam...) and has caused me to have issues with buttons registering twice. I was not aware that sometimes games had different controller functionality on different stores. Is there some requirement of this on Steam?