I'm sure you realize that the pathogenic bacteria in question is C.Diff and a different species (and genus) from the beneficial bacteria supplied by the probiotic supplement/diet and they will never interact genetically.
It is the imbalance not the presence of these organisms that causes problems. E. Colli is another common troublemaker that lives in all of our bowels but is more easily dealt with than C. Diff. While some resistance to antibiotics *might* manifest, that resistance will be lost as the individuals die off from other means. Some temporary antibiotic resistance among the general gut flora population would be beneficial to the patient in that it would help maintain a diversity. The goal here is to balance the population diversity of the gut flora including the C. Diff. The C. Diff won't go away...ever.