Usually when you're trying to repopulate the digestive system with good bacteria after a course of antibiotics, the best way to do it is with a supplement - like a pill. Since the yakult has additional ingredients, I would try getting a good probiotic (capsule/pill form) and see if that helps. Like a pp mentioned, look for a good one - usually the good ones are refrigerated, etc. someone posted a list of what to look for.
Again, if it was the yakult that she reacted to, I would try the capsules - that's what I thought you were talking about in the first place. If it was the capsules she reacted to, then yes, I would probably steer clear of those, too...