Yeah, the windows installation media does have something that looks like it should be able to repair the windows install (
ref), and basically, if during the Linux install to the other disk, if you in-fact did set it to use the Linux disk's MBR for loading GRUB into, fixing the Windows install shouldn't touch grub. If for some reason you didn't and repairing the Windows boot overrides the first stage of grub, you can always use the linux livecd to fix grub or do the repair manually