To the best of knowledge, kefir doesn't replace good bacteria. As far as I know, no bacteria in probiotics permanently colonize the bowel. They only hang around for a week or two. I would expect the same with kefir. I'm not knocking kefir, it helps lots of people by adding good bacteria, but I don't think it permanently replaces good bacteria.
Another thing you need to be careful of, is that many people with leaky bowel are sensitive to lactic acid (esp d-lactate) creating bacteria. Lactic acid can irritate the already damaged intestinal lining. This is perhaps why some people cannot handle kefir and most other probiotics. Allergy to the yeasts in kefir is another problem.