That's a personal decision and totally up to you. Like others have said, I would be more concerned about if the mare is okay to carry the pregnancy, rather than the "inbreeding" per say.
I know it isn't quite the same thing, but I found it curious that my Fox Trotter's sire is rather, um, "linebred."
Sun Dust E Missouri Fox Trotter
Notice Lady Anne, dam of Sun Dust E., is also his grandmother, so she was bred back to one of her grandsons to create Sun Dust E. I'm sure that was done because they were really fond of the bloodlines and wanted to concentrate them and create a breeding prospect. At least that's what I assume anyway, lol!
So I guess I wouldn't be so quick to abort the foal as some other folks, but hey, that is a decision only you can make because it is the one you must live with. What's right for me or what's right for someone else may not be right for you. Do what it your heart you feel is correct.
Also, I don't really buy into the whole "marketable" thing. I think horses are here to be enjoyed and make our lives richer. Not everything has to be created with marketing in mind, does it??? I guess Mustangs aren't very marketable, nor grade horses, but I sure love the ones I have and wouldn't trade them for anything. Not everything in life has to be a money maker does it? One extra horse (and probably a registerable one at that) will not break the whole equine economy. Just my opinion, I'm sure many will disagree.