How can I replace Apple Emoji font on El Capitan from Sierra?
Even if you replace the system emoji font, this won't help with all emojis. This is because some emojis are combinations of characters and this may not be interpreted correctly if the codepoints are new.

If you still want to replace the emoji font, you need to disable System Integrity Protection to replace system files.


  To disable System Integrity Protection, you can do the following:
  
  
  Boot into the Recovery HD by restarting whilst holding ⌘R.
  Open Terminal (from the Utilities menu).
  Run the following command in Terminal:

csrutil disable

  Restart.
  


Source: Disable OS X El Capitan Rootless and permit write actions to System Integrity Protection locations