I imagine the issue is two fold:
One, the game files are Blizzards intellectual property. They don't want people modifying them. It is easier (and more solid legally) to make a blanket rule to forbid it then say "oh, it's only okay if you're doing it for innocent purposes."
Two, if someone breaks the game files, Blizzard has to fix it. I am pretty confident they don't want to have to have their tech support stuff bogged down with weird errors and bugs that were caused by people fucking with the game in ways they weren't supposed to in the first place.