You are correct, the only real risk is wasting the expensive VSL#3, not inactivating the antibiotics. It might make sense to take a probiotic while taking antibiotics, but I'd probably opt for something cheap, or some good yogurt. Maybe S. boulardii, which is supposed to keep C. diff suppressed.
http://www.ncbi.nlm.nih.gov/pubmed/20458757Jan
