Q. If using DFS-R how can I encrypt the traffic being sent?
A. DFS-R enables the replication of deltas between copies of the data and can be used with DFS-N or in isolation without DFS-N. DFS-R is used for SYSVOL replication in Windows 2008.
When using DFS-R the data sent between the servers is actually encrypted by default with encrypted RPC connections. This is documented at https://technet.microsoft.com/en-us/library/cc773238(v=ws.10).aspx#BKMK_015. It is actually not possible to disable the encryption. If additional encryption was required then IPSEC could be leveraged.