Write a script.
1. stop service 2. copy files 3. start service
1. stop service 2. copy files 3. start service
Hot patching wins, but needs good design to work in the first place.
As an industry I suspect we tend to over-engineer rather than under. There is a huge spectrum between my single person business with a brochure site and what Google or Apple needs. I'm willing to bet most programmers are working closer to the first than the second.
That assumes you can stop the service which, for many things (like the World Cup website), isn't really possible.