Can't say if Marlin would do the necessary repairs needed to make your gun right. You should give them a call.
As for scratching the brass, there are many reasons for this. It could be the inside of the receiver, where the loading gate rests against which might have a rough or sharp edge. This could be rounded, without hurting the bluing. Also could be the opening to the chamber, which also could be polished to help. Check the magazine tube too. If it's sharp on the edges where it enters the receiver, it will scrape the brass when loading the magazine.
I'd surely keep the gun if possible. A good gunsmith should be able to round and polish all the above mentioned areas for a very small fe. I've done all the above things to Marlins with similar problems, and I can tell you it takes less than an hour to completely smooth up the internals.
Hope this helps.