Re: Fire your doctor~
The main reason that I posted that link is because it explains the importance of our microbe buddies. There are other ways to restore your "good" flora(actually I should say restore your floras balance because, generally there is no "good" or "bad", just imbalances).
I would recommend making fermented foods a part of your diet. Info here, also recommend buying the book "wild fermentation":
http://www.wildfermentation.com/
And eat CLEAN! Lots of organic produce, minimal meat & dairy, no simple carbs.
Feed your flora. They don't like junk! :)
And, I've just got to say that I've been thinking about you all day. That doctor's actions are beyond belief(well, no, not really).
You stated that she is a naturopath. No way. She's an MD that has added "complementary" therapies to her repertoire because that's what people want these days.
At any rate, she should be held accountable for her actions.