There are a number of philosophies on how one should approach this. Some would suggest disabling your addons and waiting a few days until the storm subsides. Some have even said you should clear out your Addons folder, or your WTF folder. Clearing out the Addons folder gets rid of the addons, while deleting your WTF folder will clear all player and character settings. I personally go this route when I find that most of my addons are acting "buggy" or weird, or when I want to start with a clean slate.
I recently wrote an article on how you can automate the updating process, which I would recommend you take a look at, the servers are down anyway! Alright, really I would recommend reading through the comments of that post, as some of your fellow readers have some great advice and insight you may find helpful. Also, the folks over at WoWInterface contacted me in regards to their own addon updater, which looks promising as well. They have been busy testing it and have released a Windows version as well as a Mac/Linux version, both of which merit a look in my opinion. WoW Interface also released their Patch 2.4 Survival Guide, which I profiled recently. All this just screams that you've got options, so keep reading!