Re: Sure it can! If you take enough of it to kill you.
In my experience it does not kill the friendly bacterias, rather they thrive on it if not too much, of course; seen here;
http://www.greenfacts.org/en/boron/l-2/boron-5.htm
My concerns in the beginning (now 7 years of supplementing) was that it could alter the stomach acid too alkaline (stomach acid practically kills all bacterias from food if the ph is right; low ph approx 1-2)
Therefore I went from taking it in water the first year to put borax in capsules, taken right before bedtime together with vit C, ascorbic acid. That has worked well for me.
The levels one have to take to kill candida I believe is far larger than the dosages if just to to cover the RDA and such; still way under the adverse reactions seen from animal testings.
I now tolerate and digest most food easily, while before all this I was very sensitive to several types of food. I recommend taking vit B while supplementing boron in high dosages.