Probably under a new name - I’d expect MS to be in control of the “Atom” trademark and branding, and they would stop further use.

if you attempt to sell, or commercially utilize the atom name in a fork of the project, i can see why microsoft would stop you.

It's just a name, but they should be able to call themselves a 'fork of Atom'.

I'd expect them to put the project out to Apache pasture (Apasture?).