Do nothing, it is best the way it is as long as you can perform your updates. Without the silly update prompt you will get in the habit of visiting the updates thread on the forum to find out if any special precautions need to be taken on a problematic update.
Get in the habit of waiting two days after an update has been released to perform your updates. This should ensure that a system breaking update will already have a patch released by the time you do your update.
Do this instead of pressing the update button whenever the notifier prompts you to, and you will almost never experience update problems. Do not rely on the silly prompter to tell you when to update that is increasing your chances of having a bad update by a large margin. Rely on the forum updates thread to tell you what to do not some silly icon. Seriously this is the best thing you can do to ensure problem free updates.