It often pays off to keep treatment for infectious diseases affordable and easily accessible - otherwise the healthcare system incurs more costs on account of the spread of the infectious agent through the population (and note that you can have silent chlamydial pelvic inflammatory disease which can cause infertility over time despite the lack of symptoms = large social/economic cost). The Cochrane review that is referrenced by that
paper you linked was published in 2005, so perhaps its just a case of the PBS being slow to catch up?
There may well have been a rationale for not approving azithromycin for pertussis in the past (say relating to drug cost, effectiveness, costs of not treating, known side effects and the community antibiotic resistance profile). I'm not really in touch with health economics so I can't properly comment on what the reasoning was, except to say that Cochrane-style metanalyses wont always apply universally if certain regional factors (such as antibiotic resistance) are important. Chances are, though, that it was just another case of PBS slowness.