It would be part of your calculations. If all you have is that one Windows-only server app (or multiple apps that can go on the same server) among 20 servers you're going to come out ahead. As legacy servers get to be a large percentage of the total, with specialty apps that have no equivalent on the new platform, you have to think about not migrating.
It's all case-by-case, but if you want to stand up two networks for say 500 users, standing up an all-Mac system will cost you a lot less than an all-Windows system. The hardware may in cases be more expensive and you may need training for people used to Windows*, but saving on licensing and a few $40-$80K per year employees will save you a lot more than that.
* When Largo, Florida switched to Linux the training turned out to be easier than they thought it would be. Most questions were like "How do I change my wallpaper?"
What I have is client/server apps that want Windows on both ends. Does OS X have a built-in equivalent to group policy that will centrally manage the hardware settings of the computers, and the software settings of the users, or centrally manage the IPSEC policies of all the machines on the network?