Microsoft made WSL to get market share from web devs who were using Linux or Mac, so they could use a Linux shell for their development while using Windows as their main OS. I wouldn’t use WSL as evidence that they wouldn’t gut Proton support in Steam.
That being said, the Steam Deck is a very successful device that I doubt Microsoft would want to get rid of, and Proton is pretty vital for that, so they’d probably keep Proton going because of that. They might still seek to make the next revision of the Steam deck run a Windows based OS though.