A risk assessment doesn't mean that everything always happens perfectly once you've done that assessment. A risk assessment just means that you *understand* those risks and can mitigate them where they are unacceptable. Risk assessments involve assessing both the chance of something occurring and the impact if it does occur. The chance of a random emergency runway maintenance that was only known about mid-flight (after departing Sydney) or the chances of large weather changes that require additional fuel, most likely scored as a low probability. The impact when it did occur - offloading bags - would be considered lower than alternatives (offloading pax in Darwin, cancelling the flight entirely), so the combination of chance and impact, means it scored low enough to allow the flight to depart Sydney without further changes. A good risk assessment should also take into account the company's ability to engage in service recovery - the fact that Qantas can't staff their call centres to help passengers with the status of their luggage, needs to come into the equation also.
I have no idea whether formal risk assessments are done for every longhaul flight, perhaps they are. But without being a Qantas apologist, it's unfair to criticise any company for ONE particular operational event. A risk assessment is ultimately a qualitative assessment, it won't be perfect and sometimes low-probability events do in fact happen, as with this case. Sometimes you just have to roll the dice. Qantas lost in this occasion in terms of providing perfect customer service, but they didn't compromise safety. The real test is whether these kinds of events happen frequently, I know Qantas has lots of customer service failures but I don't think that offloading bags in the middle of longhaul flights is something that has been a habit.