Did your vet take any X-rays? Did kitty have an ultrasound? If not, please ask for these tests before you do anything else.
Here are some things you might want to think about before agreeing to a surgical biopsy. With any luck something will work (Iâ€™ve seen that happen many, many times) and surgery will not be necessary.
Quite often giardia does not show up when a stool sample is tested for giardia. Also quite often short courses of medication (more than just one course) will not eradicate giardia. However, people I know have had great results with one long course of treatment, so please talk to your vet about that.
If a long course of treatment doesnâ€™t help, consider trying a dairy-free probiotic as the next step. Do not use a probiotic and an antibiotic at the same time because the antibiotic will make the probiotic ineffective. If you are desperate because the diarrhea is really bad, you can try giving them several hours apart. That would give the beneficial bacteria a chance to survive.
Other possible underlying causes youâ€™ll want to discuss with your vet:
FeLV/FIV - Even if your kitten was tested for these diseases at one time, she needs to be retested as soon as possible to make sure she is still FeLV/FIV negative.
Exocrine pancreatic insufficiency (primary or secondary)
Food intolerance/allergy. Food trials can be done with single protein canned diets. There are several different versions, it might be a good idea to try grain-free formulas first. If none of those works, a veterinary nutritionist (your vet can refer you to one) can formulate balanced homemade diets with different fat contents and with and without grains for additional food trials.
Inflammatory bowel disease. Your vet can try anti-inflammatory medication to test for this possibility.
Cobalamin (B 12) deficiency
After all this a congenital structural disorder might be the only other possibility to consider and hopefully something like that would show up on X-rays or ultrasound.
I agree with you for not wanting to rush into surgery. I wouldnâ€™t either. There is a lot to try before surgery. Definitely start with X-rays, ultrasound, and a new FeLV/FIV test. Then go on to all the other things step by step. Good luck, I really hope something will work for you.