I have been looking into the new features of the new version of ASP.NET Identity 2.1 and one of its enhancements is the new IoC features integrated into the OWIN Middleware.
I managed the workaround by using autofac service locator:
app.CreatePerOwinContext(() => DependencyResolver.Current.GetService());
Yes, it is not good enough, but in the mean time, we could use object same scope as declared in autofac registration process.