I believe that it is a more effective strategy to make sure that your files are all saved before you use git commands. Since I know Atom’s behavior, I try to never leave files unsaved longer than absolutely necessary. Sometimes it can be useful to transfer changes across a pull, but that’s only to be done deliberately.
If you want to check every time you open Atom, you can do it like this:
atom.workspace.observeTextEditors (editor) ->
however, that may be destructive if you try to
Split Right on an unsaved editor. Whether you have to trigger the reset manually or can automate it depends on how well you can translate your needs into the precise conditional language of the software. The API documentation is extensive and I can explain anything you need.