We had that choice a while ago.
50 desktops 98ish, logging into an NT server.
The desktop all ran a DOS-Box app called Arev, along with a bit of windowsy stuff.
NT support went bye-bye.
Arev NEEDED a real Windows server to run as the master file server / locking service stub.
So I put in a Linux box to act as the Domain Master, a W2K box to act as the Arev server / service master, and all the desktops remained the same.