Sorry for giving you an obvious information, I misunderstood.
I cloned your repository, devtools::install your package. Then I restarted RStudio, Opened a new project with your template. The new created project has no .git folder, and is not a git repository by default. Git is enabled in RStudio (Tools > Global Options > Git/Svn).
BTW i am on Windows.
It seems I can't reproduce the issue.
I suppose you add a checkbox for git and bind to a function that would to a call to init a git repo or not.