The author of "OWIN and Microsoft Katana 101" left a few hints on his blog,

PS. With Katana, there are a couple of ways of writing a middleware class: using AppFunc, which is the recommended way and using OwinMiddleware class. Although using OwinMiddleware class is not a recommended practice, even the out-of-box middleware from Katana does use this. But with ASP.NET vNext, all middleware consistently use RequestDelegate and HttpContext.

https://lbadri.wordpress.com/2014/11/01/asp-net-vnext-middleware-versus-owinkatana-middleware/

Thinktecture Identity model has support for Eran Hammer’s Hawk authentication in the form of OWIN middleware. With ASP.NET vNext introducing a new but very similar middleware concept (changes only on the API surface and OWIN middleware can be used as-is in ASP.NET VNext apps), I took the opportunity to completely rewrite the middleware. As ASP.NET vNext is being actively developed, there could be changes and this middleware will change to react to those changes. Hence, at this point, this middleware is just for review only. Since Linus had said “Talk is cheap. Show me the code.”, I keep this blog post very short and just link to github. Your feedback is welcome.

https://lbadri.wordpress.com/2014/10/28/asp-net-vnext-middleware-for-hawk-authentication-an-experiment/

Thus, Microsoft is not completely throwing away OWIN, but just carries out a few changes on the API surface. I personally think the changes are in favor of legacy code migration (to minimize code changes in existing code), but that's only my guess.