Being that they're not your insurer they can't technically write the bike off (the government could deem it to be a stat write-off if it's damaged according to their stat write-off rules, but that's another matter). RACQ have insured the car driver and as such offer him legal liability protection - you're currently his (and therefore their) legal liability. AFAIK they cannot dictate to you what you do with your bike, but, and here's the clincher, if you disagree with what they offer you you'll need to sue the driver of the car and the insurance company will represent him in court. In court you may get what you're asking for, you may get more (doubtful), you may get less (possible, see proof/evidence point below) and in a really bad case you may get less plus have to pay the drivers legal costs and court costs.
Regardless of wether you are arguing with RACQ in court or in private negotiations, you'll need to prove that the value you expect to be paid for your machine is justified. You only purchased the machine recently - do you have a receipt? Is it for more than what they're offering? Do you have receipts for the work you've had done to bring it up to the condition it's now in? Again, how do they compare to what you feel it's valued at?
To some extent you're fortunate - you're really only asking them to cough up an extra $1000 and that probably means it's not worth the hassle of fighting you - but they're also aware that if this drags on for months you're more likely to get the shits and take what they've offered than to stick to your guns, and if there's one thing going to court can guarantee for you it's a long, drawn-out process.
I went through a similar exercise with another insurance company once and the upshot of it was that I presented to them a letter of about 12 pages containing appendices, matrices, quotations, red-book values, glass's guide values, proof of purchase, etc. I didn't quite get what I was asking for, but I did a lot better than the initial offer they made me

I did, however, have my own insurance as a fall-back if I wasn't satisfied - as it turned out I cancelled my policy without making a claim and got the policy refunded rather than the policy completing.
The moral of the story is fight, but be prepared to back yourself up with proof, and get insurance - if this had been the other way round (your fault) you'd be in a much worse situation now. Good luck and let us know how you get on.