Yeah, when I was talking about parasites earlier I was being too general. What I should have said was that I was hoping to introduce them to microorganisms found in the wild, not necessarily parasites, which are the ones that do harm.
I was misguided that a higher parasite load with the animal thriving with a boosted immune system was a good thing, though. They aren't actually healthier, their area to live is generally larger and they tend not to get reinfected. In captivity, the problem is the parasites reinfecting the host, so if the load is high and they have nowhere to escape to, they will be stressed by the parasites (and additional captivity stress) which actually weakens their immune system.
At the moment, I am taking precautions and spot cleaning poop until the bioactive system catches up and washing the water dish with soap and water and replacing it with fresh water daily. I'll let you all know how the fecals go.