Nuclide (https://nuclide.io) is what FB uses/develops internally. I think even if the original team departs, they are going to be just fine. They could hire the original team right away if needed.
MS wouldn't pull the team; it would be GitHub that pulls the team. GitHub is operating as an independent company.
A fork won't have the same team working on it, a fork won't have the same domain knowledge over the internals, a fork won't have the roadmap or what was currently planned and how to do it, a fork won't have the same unified development effort (if MS "kills" atom, FB won't be the only one picking it up, there will absolutely be others that won't like the direction FB is taking, and now you don't just have Atom, you have AtomFB, Atom2, NuAtom, etc...)
It won't be that big of a deal at the end of the day (it's not like there is a shortage of competition in this area), but I would be much more on-board with this if MS handles Atom well.