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.)
3) Github has renderers for multiple formats if this language ever took off, not unreasonable for them to add one to the pile.