The mdadm superblock is placed toward the end of the device/partition rather than at the beginning. This is why it was still being detected as a RAID device (Windows just hadn't happened to write data that far in to the device yet). Also, if mdadm is still able to read the superblock, I would think it would be safe to assume that Windows/NTFS still considers that area of the device to be "blank", and therefore doesn't think there's anything there that matters. Meaning, it should be safe to zero it.
I've had to zero the superblock on devices containing other linux filesystems before for the same reason and it has never caused any problems or corrupted the filesystem.
DISCLAIMER: I don't know enough about what's contained in the superblock to say for sure that it would always be corrupted to the point where it couldn't be read if Windows had touched it, so use this advice at your own risk. Just pitching in what knowledge I have. Glad it worked out for you!