You have a heterogeneous enterprise network of servers. You want your Linux machines to communicate and transfer files with your Windows machines. You do not want to use Active Directory. What do you do?
1. Install Cygwin on the Windows server if it has not been set up already. If you need assistance with this, see this posting.
2. Open Cygwin and and set up SSH keys as you normally would. See this article How Do You Set up Passwordless SSH from One Server to Another? if you do not know how.