The overdrive theory is a traditional one...but keep in mind nobody has proven that Crohn's is due to an overactive immune system. Actually, recent research shows just the opposite: that Crohn's patients have underactive, not overactive, immune systems.
This could mean there's just enough inflammation to fester, but not finish the job of eliminating whatever is causing the Crohn's. ALL doctors agree Crohn's patients have some sort of immune system dysfunction - it's out of whack but they don't know why.
Sooo...since docs can't figure out how to cure Crohn's they use meds to tamp down the inflammation where it is doing damage. Unfortunately even where damage isn't being done, the immune system is suppressed. Also, the meds deplete vitamins and minerals, causing more immune system issues.
So yes, it needs to be boosted -- or maybe a better word is "regulated" - by yogurt, healthy food, supplements like vitamin d3/folic acid/B12/iron/zinc - it's a good idea to have blood tests done to discover deficiencies.
"Boosting" or better regulating a body's immune system does not mean you are doing things to trigger Crohn's inflammation. And you don't have to worry about vitamins, healthy food, etc, getting in the way of the meds. It just doesn't work that way. If anything, my daughter's protocol has helped the meds to work.