Are there instances when you recommend against a kidney biopsy in a patient with a single kidney who otherwise has indications for a biopsy, consents, and has no medical contraindications for the procedure?  

I don't think so. These days the risks of having to do nephrectomy after kidney biopsy is very small and having a single kidney is a weak argument for not doing kidney biopsies. In my practice, a patient with a single kidney would get biopsied by interventional radiology to minimize the risk as much...