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.
Eventually, though, they might want to allow an easy transition to VS Code in some way to cut redundancies but doing it too soon would anger too many people. Atom seems to be losing market share anyways.