Finally there is free application being released on cydia repository which allows you to uninstall and delete applications installed from cydia repository just like you delete applications installed from app store. It provides the cross symbol over cydia installed applications too with you can directly delete them from the springboard.
In order to uninstall or delete any app installed from cydia repository, hold a springboard icon down and tap on the X to uninstall. [ as shown in the image below ]
CyDelete developed by Dustin Howett is available in BigBoss Cydia repository.
Found In: Cydia BiggBoss Repository Cost: Free