I've had the same worry with mine (she is 3). She's had a few courses now for her lungs. We did the same, we held out, explained to the GPs we were not fans of antibiotics, but caved in when she regressed.
The things we did were.
-only let her have sugar from organic milk & yogurt (which she had everyday), & organic berries.
I would be really interested in suggestion of others.