@Sjakon I've flown Qantas MEL-SYD-JNB the last 2 years. As others have said, I'm not necessarily a fan of Qantas - and always look for better options. Have had bad experiences with them in recent times - twice they have cancelled my bookings (confirmed and paid for) without telling me - only discovered when I went to check in.
These were not flight cancellations - they just cancelled my booking. Hours of agro on the phone from overseas to get sorted - last thing you want to deal with at the end of a trip. These were NZ flights, not SYD-JNB.
The timing of their SYD-JNB fliight (depart ~0930) means, in my experience, it is very high risk to try and get the first MEL-SYD flight of the day and try to make the connection with firearms.
So that means going to SYD the day prior and staying overnight - all a bit of a hassle.
I allowed 3 hours at SYD (having flown up the day prior) this year, and didn't have much time to spare. AFP can take a long time based on my recent experience.
But - if you go Qatar, you'll cop a stopover anyway - and my thinking was to cop the stopover here in Aus - rather than Doha with firearm / ammo.
The Qantas SYD-JNB-SYD flights were OK - and no real issues. Got a business seat with points last year - that was very good. Just be aware that some of their cheap fares don't allow points upgrades - yet another bit of airline skulduggery.