They (both Microsoft and ActiBlizz) pulled games from Steam before, and they're both back on Steam well ahead of this deal. I don't see why that would change.
There's a lot of tangible reasons for Microsoft to pull the plug on Steam game sales.
They want to focus Microsoft products as "Cloud-First" wherever possible, and selling copies on Steam hurts this initiative.
They would probably prefer to not give Valve 30% revenue on every game sold for IPs that they own and have their own means of distribution (and even more now that they own Battle.Net) For all businesses, this is simply a case of maximizing profits.
They aren't happy that Valve are essentially letting people run native windows applications on non-windows platforms.
They view the Steam Deck as a potential competitor to the Xbox or other mobile game initiatives they might have.
They would still love it if we all used Windows Store for downloads wherever possible, which is why they have lately been streamlining the process of getting products on that storefront.
Those are reasons. I don't know if they would actually follow through and there are reasons for them to not do it, but every decision is a case of weighing the negatives and the positives. It really depends on if Microsoft cares about the public perception of forcing people to use their own store or not. Currently, they do care about forcing people onto clients, but that might not always be the case forever.