For the next pair you get, you need to be pre-emptive. When she is done with a practice or game, take the shoes off, stuff them with newspaper, and let the paper absorb the moisture and odor. We do this with all of DS's soccer cleats, and he's in them 5 days a week on average. Once they are dry, he puts an odor eliminator ball in each one when he's not wearing them. He does this with his outdoor cleats, and his indoor shoes.
For these shoes, this is what we just did with a pair he had that was NOTORIOUSLY stinky. Put each shoe in a 2 gallon size zip top bag. Put them in the freezer, yes, the freezer. Keep them there for a day or two. The cold helps to kill the odor. It worked fairly well for us, and lasted about a month or so. He has since outgrown those cleats, and Nike has allegedy fixed the problem, so hopefully that won't happen again.