You can change your flight number on your booking by simply asking Qantas. I changed this exact flight in March this year from BA 7352 to QF 52 by asking the guy at the ticket counter at Brisbane airport - he did it on the spot for me (but the ticket did have to be re-validated with a $25 fee). I did this for the express reason of being able to register for a business class upgrade (which of course I didnt get) and also to get the full allocation of points which you dont get under a BA booking for discount economy.

I wanted to also ask this forum - do you think it would be possible to change the flight number for all BA flights that are code-shared with Qantas but booked through BA? Qute handy for someone like me who lives in London and often flies BA around Europe on the cheap (but only gets 25% of the points).