Both of my daughters also had UTIs as infants. They each had VCUGs and indeed they both have vesicouretral reflux due to slight congenital issues. Undoubtedly because both of them have it, there is some genetic component to it. That said, we, like you, were very uneasy with having our baby on antibiotic. We took them to get through the first UTI (which of course had progressed to a kidney infection). We decided to hold off on the prescribed prophylatic (ie daily even when without UTI) until her next one. The problem with recurrent UTIs in children is that they are known to have complications which produce awful adult issues due to scarring in the kidney (high blood pressure, subsequent heart issues, kidney failure). I read one statistic where recurrent childhood UTIs (prior to antibiotics) were a major cause of these diseases in the adult population. The other problem with daughter #1 was that her VCUG diagnosed her with grade III/IV reflux which is fairly severe. We kept her on antibiotics for about a year (1-2 years). The good news is that most kids grow out of their reflux (around the time of potty training- because the same muscles that allow your child to control their urine is the same muscle that can strengthen the faultyconnection between the urethra and kidney) as both of mine did. We decided with #1 that the risks of recurrent UTIs far outweighed the risks of low level daily antibiotics. Given that we are really into the natural parenting styles it was something we thought carefully about but given we wanted our daughter to not be at risk for kidney-related issues as an adult we turned to antibiotics. Both she and her sister (grade I/II reflux) have not had UTIs in a long time and the eldest (with the most severe) has completely resolved her issues.
Two UTIs in such a short period would be a big red flag to me. If it were me, I would treat the UTI as efficiently as possible (antibiotics) as the risks associated with recurrent UTIs far outweigh the risks of antibiotics. Unlike when you or I get UTIs, your baby can't tell you when she is getting one, and it is only when it has proceeded to a kidney infection that you can tell.
Feel free to get in touch with me personally if you want to chat.
Good luck!
K.