How can I replace the Mac Mail icon in Mac OS X 10.11 El Capitan?
The proper way is to:


boot your Mac to Recovery Mode by holding CMD+R at startup
Go to Utilies and Terminal in the menu
Type csrutil disable and Enter
Restart normally and change your Icon


Repeat the procedure to re-enable System Integrity Protection (SIP or Rootless) but this time, enter csrutil enable

that's it !