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I know this is old but I just jailbroke my iPad and this was annoying me. I found a solution though. You need to delete the following from 2 places:

<key>cellClass</key>
<string>PSBadgedTableCell</string>

It will be in Preferences.app/General.plist & Preferences.app/Settings.plist. In the Settings.plist file search for "general" and you will find the right section. In the General.plist file it is the second <dict> group.
 
I'm surprised nobody mentioned using Springtomize 2 then turning on 2 Tap Clear Badge.

It's under the Icons settings. Basically tapping an icon with a badge twice in wiggle mode gets rid of said badge.
 
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