Goldenseal (fresh, potent, live) is a natural antibiotic.
So, yes, it runs the risk of removing natural flora.
You can use probiotics during or after the treatment (some practitioners recommend during, some after...) to replace lost flora.
If you want to be especially careful, or if the treatment is going to last awhile, you might consider using an anti-fungal, so that you don't fix your bacterial problem and give yourself a yeast problem. If you can get an anti-fungal probiotic, so much the better. I can't really say if Primal Defense qualifies.