One thing about the Confederate flag is that it's a very lively and cheerful design. So one option for decontaminating it could be to switch the colours around. Here is a site with a few specimens of how that could work . I rather like having the pink in there, which would really freak out the nasties. (Only national flag with pink is the old Newfoundland Tricolour.)

With different colours and the same design you've got a nod to the regional and cultural associations, but a rejection of the racist ones. A similar effect comes from the version using the stars, and the original colours,but laid out as a Peace Symbol, that is down the page on the Southern Students Coordinating Committee site from the Sixties I linked to a couple of times in this thread.