I agree that theoretically this is possible, and may be the best approach in the future, especially if the bad bacteria are not just in the small bowel. Prof Borody said to me that one day they will have highly specific probiotics to treat particular pathogenic bacteria and bowel conditions.
However, unfortunately this is still Science fiction. Probiotics can be helpful, but it is very hit and miss, and you usually have to take them for 3 months to find out if they help.
Of all the current probiotics, I like Bacillus subtilis the most, but everyone is different. It's hard taking probiotics at the same time as antimicrobials though. I would like to find an antimicrobial that kills my pathogenic bacteria (and yeast) but does not kill Bacillus subtilis.