What a shame, especially so soon after you got your car; I'm sorry.
I bought my '13 used from a dealership, and there were a couple chips and a few scratches on it. Some had been hit w/ touchup paint, and some hadn't been addressed at all, but I didn't notice them until I got the car home. The worst one was on the back bumper, about 4" long, and poorly painted with paint that didn't come close to matching in hue or texture.
Here's what I did..got one of those touchup paint pens from the dealership ($15?), sanded down the high spots of the previously poorly applied touchup paint (using very small pieces of 400 grit sandpaper glued to a pencil eraser.. think mini manual dremel tool), cleaned up all the spots with acetone, then dabbed on many very light coats with the pen over a period of a day or two until the paint came up to the level of the existing original paint around it. I don't notice any of them except for the back bumper scratch anymore. I did that over a year and a half ago, and there's been no adhesion issues and no rust (two of the spots were low and on the wheel well lips). Even the back bumper is much better.
Before dropping $1000 on that scratch, it's worth at least giving it a try. If you don't like the results after living with it a few weeks (the pain WILL fade...
), then shop around for another quote. $1000 seems stiff.. maybe $500?
Good luck. It's great car. Yours just has a little more character now, that's all.