I'd look into writing a shellscript/ batch file using a command-line zip utility. For example, on Windows using 7zip, the following should achieve what you want:
Code:
for %1 in (*.epub) do 7z d "%1" iTunesMetadata.plist
That, saved as .bat, should cycle through every .epub in the current directory and remove the iTunes metadata file. Though, as a word of warning: This isn't tested, so there might be errors before it works, but the principle should be right.