I don't think this change was to intentionally block this repo. In OS X 10.11, more system apps including Messages.app has been white listed for SIP protection.

I don't think this change was to intentionally block this repo. In OS X 10.11, more system apps including Messages.app has been white listed for SIP protection. Everything works if you disable SIP protection. It is understandable that Apple doesn't want malware to easily read people's messages.