T.H.
I really wouldn't worry. If you haven't skipped any pills at all, even leading up to your surgery then you're fine. You didn't even take one placebo pill right? I used to do that all the time! I never had a problem, but breakthrough bleeding is normal when you skip the placebo week, annoying, but pretty common.
As far as following your doctor's advice, well I guess I probably would do what she says b/c it will probably put you back on a "normal" cycle. That being said, I don't think you're ovulating if you've been taking the pills exacly like you're supposed to so you don't need back up. However, you may want to actually phone your doctor's office and at least talk to a nurse to find out exactly why she's having you do all this so you know what to expect.