Ive just thought of this so i dont know how well it works but you have one timer interrupt which runs once every period of the pwm frame and that simply set the pwm output high,loads the second timer with the on period and enables the second timer interupt.The second timer interupt sets the pwm output low and stops the timer running.I am sure you get the idea.The value for the second timer depending on the pwm value you want to output.It wouldnt work for small values because of the interrupt latency.It might be worth thinking about,then again it might not ;)