I think I understand your point, and it's been a while since my MCSE expired, but unless Cygwin has improved a lot I would estimate a VM wrapped by Windows would be much easier to manage and admin.

Now if you're saying that the webapp itself would be required to be a Windows process, there's really no way around that. But as I implied elsewhere, the biggest stumbler for Rails on Windows has always been the lack of a compiler. Whether you compensate for that by installing a subsystem with that capability or by using a VM with the capability is largely a local problem to the company.