IO Pin to be low after OS boot

The ethernet controller of our hardware has an enable pin (active low) which I currently enable (turn low) from the application. I found that the LCD display and LED backlight is turned ON under OS control lately.

Can I make an IO pin low under similar OS control like LCD display which will automatically go low after the OS boots up? Which registry setting is required for that?

You can use the pin.XX config block setting:
http://developer.toradex.com/knowledge-base/gpio-config-block-settings#iMX6
to configure the state of that pin at boot time.