Tagging system files
I would suggest doing what @Lauri Ranta proposes : doing this with xattr

Using xattr -wx com.apple.FinderInfo "$(xattr -px com.apple.FinderInfo 'file1')" "file2"
you can copy the tag from file 1 to file 2. 
Since /System/ is not writable for users, you just going to need to use sudo. 

Edit:  To see the tagged files, you'll need a Finder with root access. 
You can get it as using : 

killall Finder &amp;&amp;udo /System/Library/CoreServices/Finder.app/Contents/MacOS/Finder

/!\ But Warning. A Finder with Root access is very dangerous and you could easily destroy your system. 

Edit2: With the Root Finder you can directly change the tag without using the command line. But Again, root Finder is baaaad.