Make sure you are using Device OS 2.0.0-rc.1 or later. There are bugs in 1.5.2 that will cause the Boron to use much more current in sleep mode than it should. That's the most likely cause of excessive power consumption, not the LED.
However, to get the LED to turn off completely you need to disable charging as well as disable the charge safety timer and PMIC watchdog. This code is for the Electron but it should work on the Boron if you substitute Wire1 for Wire3.