I would be extremely concerned about the diarrhea. If it is true watery or pudding like diarrhea and not just soft mushy cecotropes, that is considered a true emergency with rabbits.
http://www.bio.miami.edu/hare/poop.html
And if it is true diarrhea, I personally would stop the yogurt and possibly the antibiotics as they could be the cause of the diarrhea. With antibiotics, if your rabbit is getting sulfatrim, though this is usually well tolerated, some rabbits can have an adverse reaction to it(I had a rabbit die from it). Diarrhea can be one result, and this usually means that pathogenic bacteria is taking over, and this can be extremely harmful very quickly, so needs to be addressed immediately. I would request a change of antibiotics with my vet, and I would want that change to include metronidazole to cover the possible cause of the diarrhea being enterotoxaemia caused by the bacteria clostridium sp. Questran is also recommended to absorb the toxins created by the bacteria.
http://wildpro.twycrosszoo.org/S/00dis/Bacterial/Clostridial_enteritis_rabbits.htm
Rabbits can't properly metabolize dairy products, and though yogurt might be recommended by some, it's clear your rabbit is having an adverse reaction to either the yogurt or antibiotics, and since you can't determine which, I would stop both and consult with my vet. I would personally go with the bene bac as it is a much safer option to provide probiotics to a rabbit. With the amount of bene bac to give, I would just guesstimate what is going to be the right amount. If a tsp seems too much, give a little less. Better to start out with a little less to make sure there are no adverse digestive reactions, then increase if there are none and you feel more is needed. And it's not like a medication that has to be given in exact amounts. Though do keep in mind that there are sugars in it, so that has to be taken into consideration.
http://www.bio.miami.edu/hare/ileus.html
Because sugars and starches will 'feed' the bacteria, it's also usually recommended removing pellets and any other starchy/sugary foods, and free feeding some sort of grass hay only. This helps with restoring the normal gut bacteria. If your rabbit isn't eating well on it's own, I would syringe feed a slurry made from hay or hay pellets.
Though your vet does seem knowledgeable about rabbits in some respects, one thing I have learned about getting the right treatment for my rabbits when they are sick, is that I have to be their advocate and become self educated on what is usually considered the correct treatment for their various illnesses, and that I can't just leave it to my vet and trust they know what they are doing. I've experienced and read of too many instances of misinformed or under educated vets prescribing the wrong treatment for a rabbit, sometimes with fatal results. I really hope your vet will listen to your concerns and work with you to help your rabbit get well again.