Only just saw this thread. Like everyone said, glad Tha you are ok!
Its sad to have to total a bike just for cosmetic damage. I'm guessing the insurance company's repair quote is using new genuine Honda parts and labor. Have you looked into replacing with used parts and/or Chinese tupperware?
For instance, ebay has a used saddlebag for $250 vs. +$800 for new parts.
RIGHT SADDLEBAG ASSY.
www.ebay.com
Here's a full fairing kit for $250:
Find many great new & used options and get the best deals for Motorcycle Unpainted Fairing Kit For Honda ST1300 2002-2013 Bodywork Panel Set at the best online prices at eBay! Free shipping for many products!
www.ebay.com
Or a little over $200 for just a used right fairing in you want to paint it:
Find many great new & used options and get the best deals for 2006 03-09 Honda ST1300 ST1300P Right Side Fairing Cowling Panel Cover Trim at the best online prices at eBay! Free shipping for many products!
www.ebay.com
You could wait on the muffler.
You could probably fix it for much less than the insurance company quote.
That being said, having the insurance company square off your loan and starting over isn't a bad deal either. A new ride in your stable will greatly help to smooth the sting.