But does it actually not work? There are some apps that have a popup about it being "unsupported" but it still works fine (Skype is the most famous example).
Originally Posted by Static_FX
If its actually being prevented from running, what you need is called xCon: http://www.ijailbreak.com/cydia/bypass-jailbreak-detection-errors-with-xcon-cydia-tweak/
Added bonus: the dev has been good about both suggestions for additions and keeping up with app updates that require xCon to be updated.