$MFT isn't accessible from user-mode programs. (Thank god.) It's maintained by the NTFS driver, and the NTFS driver alone knows how to keep it up to date.
For your planned implementation, I'd suggest either using the file system directly, or implement a file system filter driver. There's a tutorial on writing a file system filter driver, and some pointers on detecting deletions. (As always, there are some tricky bits...)