How do you stop Atom from interfering with git?

#1

Atom 1.36.1
Git for Windows 2.19.1
Windows 10

I’m just about at my wit’s end with Atom’s insistence on integrating with git. If I try to run any rebase or fetch or merge command in the terminal, I get errors like this:

warning: unable to access '.../.gitattributes': Permission denied
warning: unable to access '.../.gitattributes': Permission denied
warning: unable to access '.../.gitattributes': Permission denied
warning: unable to access '.../.gitattributes': Permission denied
error: cannot stat '...': Permission denied
error: cannot stat '...': Permission denied

If I shut down Atom and try again, everything works fine. Similarly, if I run git gc --aggressive or even just git gc, I get errors like this:

$ git gc --aggressive
Enumerating objects: 85169, done.
Counting objects: 100% (85169/85169), done.
Delta compression using up to 4 threads
Compressing objects: 100% (78986/78986), done.
Writing objects: 100% (85169/85169), done.
Total 85169 (delta 58655), reused 24885 (delta 0)
Unlink of file '.git/objects/pack/pack-055d2bae456e80a156d67d6a959c4d69a5710276.pack' failed. Should I try again? (y/n)
Unlink of file '.git/objects/pack/pack-0dfc634fa1886edce35dcddf38633cf35fca7aa8.pack' failed. Should I try again? (y/n)
Unlink of file '.git/objects/pack/pack-10ce79b20a39b053ba78edd758323d08b6197a60.pack' failed. Should I try again? (y/n)

If I try to delete those files manually in Explorer, Windows tells me they’re open in Atom. If I shut down Atom and run the garbage collection again, everything works fine. WTF Atom?

I’ve already disabled the git-diff and github packages. Is there anything more I can do to stop this intrusive git integration beyond moving to another editor?