This is a common problem when users try to customize a theme. In some of my themes I include an option to easily insert custom stylesheets. Maybe you can do a pull request to add the following scheme to the theme:
Inside the config file I assign an array to a variable:
[params]
custom_css = ["css/foo.css", "css/bar.css"]
You can reference as many stylesheets as you want. Their paths need to be relative to the static
folder.
Inside the header partial you can include every custom stylesheet from above beside the original one:
{{ range .Site.Params.custom_css -}}
<link rel="stylesheet" href="{{ . | absURL }}">
{{- end }}
This way you don’t touch the header partial at all but you’re still able to overwrite CSS classes.