Filtering noise off of PWM signal
You can still use a low pass filter but you might need to use a higher order filter in order to reduce the switching noise of the PWM. I'd place a low pass filter between 1 ohm resistor and input to the amplifier just to kill-off the bulk of the PWM noise and then after the amplifier maybe add another low pass filter. I take it that this will then feed some micro controller - if so the MCU can perform digital filtering to reduce noise even further.