I was experimenting how strong SIP is on Sierra. So I tried To delete Terminal.app using app cleaner but I can remove the contents then when I empty the trash it empties it. Then I open terminal App it works Fine.So is SIP that strong that you can't remove an OS X app using third Party apps?Is the only way to remove SIP protected apps using rm command?
Third party tools and
rm can not delete System Integrity Protection (SIP) protected files.
To remove Terminal.app from your Mac, you would first need to disable SIP.
System Integrity Protection on your Mac means you can not delete or modify a range of important files and applications. See About System Integrity Protection on your Mac for what and how SIP protects you.