What are you talking about? Let's take it point by point to battle the FUD.
most business software is Windows only
Large businesses using linux: Walmart, IBM, Redhat, Amazon, Rackspace, it goes on and on...their ERP software is web based running on Linux.
Linux has nothing to compare to Active Directory
You realize Active Directory is a *broken* implementation of LDAP - something that has nothing to do with Windows? The enterprise world uses IPA, Radius, and OpenLDAP. It's light years ahead of Active Directory, and actually follows RFC's(Active Directory does not).
Linux has lots of advantages, but manageability isn't one of them
There is no point and click "management" of Linux. You actually have to know what you are doing. You don't get to buy a for dummies book or take a night class to be rewarded with an "admin" job. A good example in some large(1000+ employees) enterprises I've worked for is deploying [Linux] login scripts via directory services. It allows control and lockdown of user settings and permissions in ways Active Directory cannot hope to. You mentioned Puppet also - that's a server management thing though, not a user management thing. It's good you mentioned it though...where is the Windows equivalent of that? Powershell? VBScript? Doubtful.
The world is changing man, typical users are not baby boomers anymore that have a limited computing skill set. They are intelligent, capable of learning new technology. If they aren't - they get replaced by people that *can* do those things, because those things are in the interest of the business. Stop the FUD.