That's surprising and sort of disappointing to me. I _just_ (within the last week or 2) was setting up my $HOME to be .git controlled...and was thinking "Maybe I should give Atom another shot"
The GitHub issue the I created for Atom was closed almost right away with the comment that this problem has been fixed in the Atom 1.5 beta.
That's good to know, next time I'm evaluating whether to switch text editors (which happens plenty) - I'll have to keep that in mind (or more importantly try and not discount Atom immediately because 'Oh yeah, doesn't it have a problem with $HOME/.git?')