This reminds me of the format fragmentation going on in the 80s, when on the same day you could find certain country music acts only on cassette, vinyl, or 8-track, and alternative rock acts only on cassette, CD or DAT (remember Rykodisc? Its claim to fame was to be the first label to eschew vinyl).
I can imagine the major labels cutting off certain physical media for certain artists when it's established that there are effectively no sales going on there, since manufacturing and warehousing disks costs money. If an artist's online sales are some large multiple of her CD sales, then CDs are effectively continuing to be manufactured more for the promotional reason of having things in record shops to stay in her fans' eyes, because CD sales' contribution to the bottom line isn't going to be meaningful.
The major labels have done a lot of stupid, antagonistic and dunderheaded things with regards to digital media and fan behavior, but underneath all that there's still some pragmatism to be found.
Trent Reznor observed a few years ago that CDs are effectively a pointless medium for music sales since you can get the same music faster, better and cheaper online, but that treating the CD or vinyl LP as more than just a vessel for sound files can continue to justify its existence. So Nine Inch Nails' recent albums have all been visual and tactile experiences as well as music media. I'm not a NiN fan, but Reznor is a canny businessman and has a good sensibility of what he needs to do to keep his fans happy and allow him to continue being a productive artist, and I respect that. Other musicians and labels have been paying attention, and even Capitol Records has issued The Smile Sessions in a couple different editions, ranging from a $30 2-CD box with booklet, poster, and pin to a $6,000 5-CD, 2-LP, 2-single package with hardbound book, lightbox sculpture and full-size surfboard.
You'll be seeing more things like this in the coming years. I don't think the CD is going to go away, but I suspect its status as the primary distribution medium for A-list and B-list major artists is going to change.