For a built stable machine I am sure NTFS is a wonderful addition to the security if the owner of said machine operates as per the dictates that microsoft want. Which I suspect only ever happens in an administrated network. And almost never in the home environment.
We are talking about cleaning a diseased box of tricks. Which I suspect has been operated in power user mode if not admin on the main user account. It would explain the turning off of the anti virus and also installing games. Which I suspect the issue was with some crap updater for the game getting flagged as malware.
By transferring onto FAT32 then putting back onto NTFS if you so wish you strip all the extras of NTFS, all the ownership problems are gone. It is just a tool to get a job done of restoring a machine.
I must admit thankfully I have only ever worked with networks using Samba to link through onto the unix file servers. Now if you want true security and performance that's the way to go.