Great to see you got a better routing, and completely understand the need to not have so many connections and long layovers. Not everyone is crazy like me in that regard.
Would you rather have the points back or would you rather fly in business up to Brisbane? Personally I'd take the business class seat over the refund on points which I suspect would be very minor in the grand scheme of things. Sure it'll be a 737 so no lie flat seats, but you'll have a better meal, fewer neighbours and of course access to the Perth business lounge which I reckon should have fewer men in high-vis jackets!
I wouldn't be too sure that this flight will credit like a revenue flight. The QF website is notorious for giving misleading information on the number of status credits one could earn. Even if the flight is ticketed as a J fare, the fare could be coded as an award fare and thus ineligible for earning status credits (unless you're a points club member).
-RooFlyer88