If rapid sterilization is a requirement of the process, than it makes sense to embedded it into the design. The 100 ton reactor could have electric heating elements surrounding it on every side, or magnetic loops that induce heating to the stainless steel vat. Do a dry pre-heat at 500K to vaporize any leftovers then fill it with clean water and bring it to a boiling point, establishing slight positive pressure against any pores or leaks. And voila, you have a sterile 100 ton reactor with zero bacteria.

Similar sterilization systems would be installed on all ingress ports, using heat, ultraviolet or gamma ray, depending on the nature and heat sensitivity of the input, with slight overlap between the different systems.

Since you are culturing organic life from dead raw materials, and life is so sensitive to heat, gamma rays etc., it seems relatively simple to make sure nothing alive enters other than what has been grown in upstream reactors. Recursively apply these principles down to the last cell inserted into the process inside a (small) clean room.