I think everything has a place. There's only enough commercial rennet to supply about 1/3 of the current world production of cheese, and that's optimistically. But compared to the bulk market, the artisan market is small. The reality of it is here's what happens:
- Smaller producers most often have their own animals.
- Producers do not keep male kids and good breeders will cull does with poor conformation. And even the most humane people generally shrug the killing of young males as something necessary to the making of cheese.
- Producers who are smaller and in specialty goat and sheep markets tend to send kids to the slaughterhouse, which wastes the abomassa because there's not much of a market (this is not true in many parts of Europe).
- Producers who are larger or who have an established veal processor n the area (here in WA state, we have one for the entire state who does most of the veal processing) will send their calves to a slaughterhouse that retains the vells and ships them to one of the major 4-5 rennet makers in the world.
- On average, it takes the rennet of two kids to process the milk of one mom. And on average cows give birth very close to two kids, completing the circle.
So with that in mind, if in the artisan scene people put in the extra effort to be full circle with their operations (not faulting those who do not and not saying they do not care. I slaughter my male kids, too), animal rennet would be the most sustainable choice for all milks. As it stands, right now it is not far off from being the most sustainable. As for fermentation produced chymosin... mixed thoughts. Engineering bacteria and yeasts to be factories I don't think is completely wrong. We do it all the time naturally by strain selection... fine line there when we "help" the process along. And the product, FPC, is so purified that it's not like there are residues. And to meet current cheese demand, it has to be produced due to the volume that modern cow breeds crank out. if cow breeds produced like they did 100 years ago, animal rennet production would be the best choice, would all balance out.