What Mac is this on?
If it's a newer Mac that supports Windows via UEFI, I believe you can use Microsoft's full drive(partition) encryption called Bitlocker without any manual steps or issues. Encrypting the Windows side would be a secure way to keep the sides separate.
If it's an older one, it's tricker as you have to deal with the limits of some of the BIOS emulation and the partition layout.
List of newer Macs using UEFI for Windows instead of the older BIOS emulator:
MacBook Air (11-inch, Mid 2013)
MacBook Air (13-inch, Mid 2013)
MacBook Pro (Retina, 13-inch, Late 2013)
MacBook Pro (Retina, 15-inch, Late 2013)
Mac Pro (Late 2013)
iMac (21.5-inch, Late 2013)
iMac (27-inch, Late 2013)
iMac (21.5-inch, Late 2013)
I'm seeing hints of people using /etc/fstab in the past to disable the auto mounting of NTFS volumes. This method might not work anymore under 10.10, and would still allow the other user to manually mount and see the files.
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