The perceptions among gamers of an all-digital X1 might be better, but in reality it's not necessarily a better deal, at least as far as game licencing is concerned.
If the X1 were all-digital, you probably wouldn't be able to sell or give away your games at all. While there are some restrictions on this with the X1, it still provides more freedom to the consumer than a service like Steam, where you are stuck with the game you buy for all eternity. Hopefully we will see even more freedoms allowed as time goes by, namely more time allowed offline and the ability to rent and borrow games to some extent. Considering all the outrage being poured out against Microsoft right now, it's not at all out of the question that Microsoft will work on things like these in order to win back some goodwill from the gaming community.
And obviously, having discs allows retailers to sell used X1 games, which means they will still have just as much incentive as before to promote the X1, which means better sales for the X1 and its games. Just selling the console, accessories, and game codes would not be good enough for retailers when the competition is still letting them sell used games. Unless Microsoft was paying retailers to make up for the lost revenue, they would give the all-digital X1 the short end of the stick.