Yes, you can write READMEs in ReST or Org, but you cannot write issues, pull request descriptions, comments, or discussion posts in anything other than GFM.
On the other hand, they already migrated GFM once (to CommonMark), so it's not wildly unimaginable they might do it again. There is precedent. (Of course, it would have to take off first. Adoption is problem #1.)
