[eluser]Derek Allard[/eluser]
Well, you should be covered there even. The nice thing about CodeIgniter is that everything (everything) runs though the index.php page, so if that isn't there, then nobody will be able to "half access" the site. Plus, the whole update should only take a few seconds, so you're probably fine there.
If it was a big site with millions of visitors, you'd want ot investigate dns tricks to redundant servers or something, but for your average business site, a few seconds of downtime is not usually even noticed.