Since spaying is a more invasive procedure than a neuter, I think having her the healthiest is best before a spay, though it’s ultimately your decision, along with veterinary consult. Territorial poops are indeed annoying, but it can be calming to know your rabbit is getting healthier as well.
For the probiotic Wick gets, it’s a powder that I store in the fridge, and I feed a sprinkle to him on a wet piece of lettuce about 1-2 hours after each antibiotic administration. This was a daily routine for 3 months while Wick fought his URI (a very pesky one; 3 months is not a normal length for treatment), and whenever he gets antibiotic treatments, like right now for his ringworm infection.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.