The supported way to disable System Integrity Protection in those cases where it's truly necessary is to boot into the Recovery partition and turn System Integrity Protection off from there with the csrutil tool.
usage: csrutil <command>
Modify the System Integrity Protection configuration. All configuration changes apply to the entire machine.
Disable the protection on the machine. Requires a reboot.
Enable the protection on the machine. Requires a reboot.
Display the current configuration.
The kext-dev-mode and rootless boot-args are being removed from OS X El Capitan and will no longer work.