If a user follows the instructions then there won’t already be a .git/ dir; if they are not following the instructions then they will need to be mindful and aware of what they are doing :)
which instructions? there's nothing that says "don't try installing this as a submodule to an existing repo"
These instructions https://github.com/csswizardry/inuit.css#installation
If someone is doing something other than what is intended then it is their responsibility to take care and pay attention.
Could the description "removes the web template’s Git instance and replaces it with a fresh one for your project" be put on https://github.com/csswizardry/inuit.css-web-template
[refs #3] Add details about what go script does