Voltage Regulation to Brushless DC Motor
The switch allows for PWM output, which I have seen can be filtered to
  an analog output voltage - however I have not seen this done on high
  current inductive loads. Is this a feasible solution?


Probably not. The pump's built-in motor controller probably has a large filter capacitor across the supply to damp voltage spikes caused by lead inductance, so the load will look capacitive rather than inductive. 

With simple switched PWM the capacitor will charge up to full supply voltage during the PWM 'on' time, and slowly discharge during the 'off' time. If PWM frequency is high the voltage will stay up between pulses and you won't get the desired speed control. To get an average of 6V the voltage must go down to zero between pulses, which may cause the pump controller to turn on and off rapidly, not turn on at all, or even blow up.

To smooth the PWM output you could add a diode and inductor, but the output voltage will vary depending on the load. To produce a stable output voltage you need to modify the PWM ratio according to the output voltage error. This is what a switching regulator does. 


  Another idea I had was regulating the output voltage of the high side
  switch using a switching regulator of some sort - not sure if this is
  a good solution either.


This is actually what you need. Depending on the device, as well as varying the output  voltage you may also be able to turn it on and off with an 'enable' signal, and then you might not need the high-side switch.