You're talking about Windows though. This topic is about Linux. I don't pretend to specialise in automation on Windows like I do with Linux but what experiences I do have managing Windows instances have all been painful (regardless of whether they were a desktop or server) because the problems require a completely different mindset to solve and half the time those solutions are only semi-effective. So I do feel your pain there.
For what it's worth, I've had some success with Powershell for package management and domain management, and tools like Clonezilla / Norton Ghost for managing images on small to medium sized fleets of machines (again, both desktop and server). There are also a plethora tools that can interrogate what machines are on a given network, the software installed and their patch levels -- but most of them are not going to be free. However there definitely are alternative options to SCCM and WSUS if they're too "enterprisey" for your needs (I've used a few different ones but I'm afraid I can't recall the names of the more effective solutions in terms of ease of us and features vs license fee).
I agree, Windows is the main difficulty here, but we also ship (Desktop) Ubuntu. It's much more amenable to command line tools, but probably still nowhere close to what people working with disposable VMs on the cloud are used to.
For what it's worth, I've had some success with Powershell for package management and domain management, and tools like Clonezilla / Norton Ghost for managing images on small to medium sized fleets of machines (again, both desktop and server). There are also a plethora tools that can interrogate what machines are on a given network, the software installed and their patch levels -- but most of them are not going to be free. However there definitely are alternative options to SCCM and WSUS if they're too "enterprisey" for your needs (I've used a few different ones but I'm afraid I can't recall the names of the more effective solutions in terms of ease of us and features vs license fee).