Can you confirm that the incoming PWM duty cycle is between 6% and 12%? That sounds a bit odd to me.
I had a quick glance at the TMC2208 datasheet, but I'd need to study it more to say something smart...so just one question: have you confirmed experimentally that the 1~70Hz pulse rate is indeed correct?
How much resolution do you need? This is going to determine the feasibility of measuring the 6~12% duty cycle of your 60Hz incoming PWM. Unless of course I misunderstood what you said about a 1~2ms duty cycle; it's kind of odd to express a duty cycle in ms instead of %.