a pattern I have seen before is to clone the branch commit of each release to a folder /var/releases/{release_commit} and then html is not a folder but a soft link so /var/www/html -> /var/releases/latest_release_commit
this is useful if you need to revert back quickly.
But then releases folder needs to be cleaned up, or you can run out of space.
Safer/easier to keep the .git somewhere else entirely, rather than in the working directory. Git's got arguments that let you do that. Then you can check out to a dir that doesn't have the .git dir in it at all.
Alternatively, it's pretty easy to use git-archive (optionally, with an exclusions list to keep out files you don't want to serve publicly) to do something similar without ever cloning the remote repo. You can fetch a zip or tar.gz with a given commit's files, straight from a remote repo.
