It seems like the consensus is that the best idea is to place the faraday isolators before the MMT. This way, we can use independent lenses to focus the beams into the FIs to avoid clipping and not have to deal with this additional constraint when designing the MMT and when adjusting the steering mirrors.
We played around with the layout this afternoon, and there just isn't enough room to fit both FIs and PDs (along with steering mirrors and lenses) side by side far enough upstream to leave room for modematching. We decided to rotate the AOM setup so that it folds back towards the laser instead of perpendicularly outward, as in the picture below.
The second picture shows that the FIs and PDs fit just fine with this newfound space.