Not necessarily because the MAP are intracellular bacteria. So since the chemo destroys all the cells in the immune system, the MAP goes with it. It's similar to the fact that they found that 6-MP and Imuran are found to be effective against MAP.
They even found 5-asa to be effective against MAP. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000516
So we could have been treating MAP all along, who knows?