One option is to set gh-pages as submodule of your own repository.
That means adding thegh-pages branch content as a subfolder of your current repository, in the master branch, using git submodule.
(unless, as explained here, you chose the master branch itself as source for GitHub Pages)
git checkout master
git submodule add -b gh-pages -- /remote/url/of/your/own/repo gh-pages
git commit -m "Add gh-pages branch as submodule"
git push
You will have a gh-pages subfolder, that you can update at any time with:
git submodule update --remote
My issue is that I am getting the directory and it's content while I need the content only on the root.
You would generate, from your main repository, the site content not in the directory _site, but in the directory gh-pages (which would thereforce have directly the site content).