Okay, so short term you should just be able to launch Atom from a
cmd window and things should work fine (hopefully).
Long term you should figure out why your System PATH is broken – by default you should have a lot more entries in there:
Not all of those are necessary I think, but AFAICT you should definitely have the
C:\Windows ones or the
%SystemRoot% ones. You might be able to find the missing ones with
echo %PATH% in a cmd terminal.