Your body doesn't know a Doctrine is running.
All it sees is a pathogen to try and deal with where just moments before was something unknown and ignored due to the toxin.
A clear example is how the Spanish flu was successfully treated with Gelsemium. Gelsemium eliminates the toxin, once gone the body can handle the virus with a little help.
"One doctor in Ohio used only the Gelsemium strain in 1800 cases with only one death. He didn't use anything else, not even aspirin."