The green LED mostly indicates reads/writes to the µSD card.
It's used to indicate other things as well. Like blinking 10 times when the RPi shuts down or different "blink-codes" to indicate things like boot errors. Like "beep-codes" on traditional PCs.
I believe the OS doesn't have much control over the status LEDs or it would be pointless anyway, because the LEDs are controlled by the hardware/firmware to indicate hardware stuff.