I take it the vet still feels its just an infection then?
I've never used benebac, but yes you can use that. I've always just purchased some high count probiotic from the human supplement section of my health food store. Open capsule, sprinkle some on her kibble, or mix it into anything you syringe feed or soft food she's eating. I think you know this, but just in case, or for anyone else reading this... keep in mind that you cannot give probiotics and antibiotics too close together else the antibiotic will nuetralize the probiotic... mid-way between antibiotic dose is preferable if you can time it right.
Soft and green can be very normal for a hedgehog on antibiotics, especially with certain types. For example, baytril is well known at causing GI upset and I always give probiotics for up to a week after they are off it to help settle the GI. Its a great antibiotic, but it can cause absolute chaos on their GI, in my experience.