C difficile rarely gets into tissue, the unbalance is in the lumen. The damage to the intestinal flora is from the cephalexin. Taking entocort or not doesn't matter.
If the microbe was in tissue then yes you'd be right, it would increase your chance to get tuberculosis for example. But c difficile is from a hospital, you touch something, you ingest it through the mouth, the bacteria survives in the colon, you then take a broad spectrum antibiotic wiping all gram+ and gram-, C diff survives and exploits this chance.
Once you have C diff, toxins do get into tissue, but the bacteria doesn't.
The gut flora is able to communicate with the immune system, and it does so 24/7, but the immune system isn't directly involved in gut flora homeostasis, that's the job of the gut flora, unless a bacteria enters tissue. There's mini lymph nodes all over the intestine called peyer's patches, they sip content from the gut lumen, and learn what's present in the gut lumen, if there's pathogens or not, but they're just waiting until somethign enters tissue, which c difficile normally doesn't do.