I think it's horrible when legitimate and honorable symbols and words are transformed into something hateful, and what we know as the swastika is the one that always comes to mind first. (It was formerly a stylized Christian cross common in the Eastern European areas and parts of Russia.) However, since the awastika has become a symbol of hate, you obviously must change the quilt, and I'm glad you're willing to do so.
Several years ago there was an absolutely elegant quilt for sale on consignment in a quilt shop in Illinois, and it was designed around a centered Orthodox cross and containing numerous Orthodox Christian symbols -- beautiful colors, exquisite work. Unfortunately, between rows of sashing going around the entire quilt was a row of small swastikas! And the quilt, obviously, did not sell, even after several price reductions taking the price down to cost of materials. The lady then tried to donate it to a church for raffle, and they wouldn't take it. It took FAR too long for her to do it, but she finally removed all of the swastikas -- and then the quilt sold very quickly. I was actually surprised that the shop owners first even allowed it in their shop, but the quilter was a relative of some sort, so they had to take it to preserve peace in the family, but they did put it in the most out-of-the-way place they could find. Had I known enough about re- working quilts at the time I might have purchased it and re-worked it when it was at its lowest price.