Optical Communication Two Sources One Receiver
I think you are almost there with the pwm idea. Keep the pwm modulation at the same frequency and then take the output of this at each transmitter and use it to modulate a much higher carrier frequency, different in each transmitter. Filter the two carriers at the receiver and you end up with two PWM modulated signals.

As long as you are not saturating the photodiode the received signal should be the sum of the two incoming signals.