Does anybody know how the headphone jack pins are controlled on the N9? Is it tied directly to hardware or could the pins be arranged by a driver?

I would like to be able to change the pin layout to the CTIA layout used in Apple iOS devices as there are tons of headphones supporting this layout. I understand that the N9 uses the OMTP layout, which has the pins in a slightly different arrangement.

I am using a OMTP to CTIA adapter dongle now, but it ruins the aesthetic of the N9.

It's a hardware problem.
You can use a cheap (hardware) converter though Just a small extension to your audio cable