Doesn't that make sense? Why would you want to run a core 2 app on the desktop CLR instead of distributing a binary? Not having suitable replacements for a lot of existing libraries is the bad part.
The issues people have with the move largely revolve around applications that need .NET Framework (such as WPF applications) which embed network servers currently built on ASP.NET Core 1.x, which runs happily in that scenario, but 2.0 won't and 1.x support isn't going to be around for more than a year after 2.0 drops.
WPF will probably never work on .NET Core, so after that they're going to have to have some kind of elaborate multiprocess solution if they want to stay in supported versions.
.NET Core 2.0 should run most libraries from every verson of the .NET Framework 1.0 to 4.6.1 (and potentially higher), with very few exceptions (albeit in some cases literally exceptions). (That's all the work that has gone into defining the .NET Standard 2.0 API.)
Yes, I agree with the guy for example needing NHibernate. It's a pretty big deal in the ASP .NET world. Anyway, here's an issue tracker for that one: https://nhibernate.jira.com/browse/NH-3807
I also agree with the opinion that ASP .NET Core shouldn't have run on the full framework to begin with to set the right expectations. We seem to be in yet a transitionary period by Microsoft and if the point is to decouple it from .NET Framework, it shouldn't have had legs in it.