You will probably have to use a DSP to sense the back EMF inbetween the pulses, and it won't be easy. Most of the available controllers filter out the pwm pulses with an rc filter on the back EMF signal, because of the noise induced when the pwm switches. TI and Motorola have some app notes for doing BLDC controllers using their DSP chips. They may have development boards that you could use to prove out your concept.
Motorola even has an app note for a controller with 3-phase sine wave output, but it uses hall sensors.