I'm pretty certain that Microsoft already (mostly) made this backward-incompatible move several years ago, when they shut down the last of their (old Skype protocol)<->(MSNP24) gateways in 2014, so any Skype clients that predate the MSNP24 support being added to Skype no longer work.

The thing they're doing now is probably either breaking Skypeweb backward compat or a rev on MSNP, depending on which mechanism the embedded clients use. Quickly reading the actual blog post that the Ars article is about [1] (which I couldn't find an obvious link to in the article) makes me think it's probably Skypeweb they're breaking.

[1] - http://blogs.skype.com/2016/07/20/skype-the-journey-weve-bee...