Hi Nick,
The MRF101 can certainly be damaged by transmitting RF power into the wrong LPF. The best way to avoid this is a systematic approach rather than protection circuitry; ie. setup the control system such that this condition is prevented either by sensing the frequency of the input signal or automatic control of the LPF by the source (radio) so selecting a frequency on the radio automatically selects the proper band in the amp.
If sufficient protection cannot be achieved through the control system a directional coupler before the LPF could be used to shutdown the amplifier if there were an incorrect or damaged filter.
If you decided that a coupler before the LPF was necessary, then you would probably still need a coupler on the output if you want to accurately measure SWR and power. That's because the LPF removes harmonic content which would be measured a coupler placed before the filter. Also the coupler before the filter would detect harmonic energy reflected LPF as reflected power so even into a perfectly matched load the coupled before the filter would detect reflected power and give erroneous readings.
So the question is not whether the coupler should be before or after the LPF, a coupler before the LPF performs one function and one after the amp performs a different function. Which functions do you need in your amp?
73,
Jim WA2EUJ