MacOS – Is it safe to disable System Integrity Protection

Apple's documentation covers disabling SIP, About System Integrity Protection on your Mac and Configuring System Integrity Protection.

An article on lifehacker.com lists these steps:

1. Reboot your Mac into Recovery Mode by restarting your computer and holding down Command+R until the Apple logo appears on your screen.
2. Click Utilities > Terminal.
3. In the Terminal window, type in csrutil disable and press Enter.
4. Restart your Mac.

You can verify whether a file or folder is restricted by issuing this ls command using the capital O (and not zero 0) to modify the long listing flag:

ls -lO /System /usr 

Look for the restricted text to indicate where SIP is enforced.

By default (=SIP enabled), the following folders are restricted (see Apple Support page):

/System
/usr
/bin
/sbin
Apps that are pre-installed with OS X

... and the following folders are free:

/Applications
/Library
/usr/local

There should be no extra step required - in fact, reading through the excellent article linked from that question, I found this…

Because SIP’s configuration is stored in NVRAM, SIP’s protection settings will apply to the entire machine and will persist even if the OS is reinstalled.

This would perhaps imply your NVRAM is not correctly holding data -
perhaps try a reset, Cmd ⌘ Opt ⌥ P R at the chimes & keep holding until you hear the chimes a second time.

Source : System Integrity Protection – Adding another layer to Apple’s security model

If after resetting NVRAM one time, you can’t make SIP status stick the next steps are to repair and wipe your drive and then seek hardware service is a freshly erased and reinstalled OS won’t allow you to disable SIP.