That would work if you can calculate the correct dosage and mix it with juice or a syrup(no artificial sweeteners). Or if you have a human compounding pharmacy that can make it into a suspension. Dosage info is in that link I posted above. But it's up to you if you want to try it or stick with the one the vet gave you.
But if your rabbits fecal poop isn't normal now and is still watery diarrhea, the cholestyramine is really the medication that has the greatest chance of saving the bunny, because it's the exposure to the toxins released by the bacteria, that result in it being fatal. If you are able to get some, it needs to be given at least one hour after any other medications. There is info in this link about meds and dosages for treating diarrhea in baby rabbits.
http://www.bio.miami.edu/hare/squirts.pdf
If your bunnies poop is back to normal and the bunny is eating on it's own again, it may have been some bad food it ate and it may be ok now. But definitely avoid grain foods and sugary foods. A good quality hay(no mold, no noxious weeds) is the best thing right now to help correct digestive upset issues, if the bunny will eat it really well.