[eluser]Daniel Moore[/eluser]
For 99.9% of sites, the performance issue won't matter. You are right about that. As I stated, if it's not a high traffic site, then it would indeed be best to do it your way on that one. For a site with millions of hits, you will need the most efficient code possible, because every line that has to be loaded by the server is another hit on that server's processor. Eventually it will catch up with you if the site is a high traffic site.
For lower traffic sites, it's all just a matter of personal taste, but would be best to put it in the hook as you suggest.
Even on a high traffic site, if you decide to do it in the index.php file, there should be some sort of documentation, perhaps in the hooks.php file, that would point you back to what you did should you need to revisit this in a couple of years, or should another programmer take over for you and need to figure it out.
Using a pre-hook would be the proper "CodeIgniter" way to do it for sure.