There's a lot jailbreak tweaks that would get this done. (I assume you're not updating because you're jailbroken.)
Oh, sorry. I'm not jail broken but want to when the next one is released. I'm hoping to stay at 9.1 just in case that is the version released. Probably not the best place to ask but I had the reminder pop up while checking on jailbreak news...Mikoto. It will remove the badge and also physically prevent you from accessing the actual update mechanism. You'd have to uninstall Mikoto on purpose in order to "accidentally" update.