You cannot remove the jailbreak fully from a device by any other method than a "restore" in iTunes. Removing Cydia or other components does not un-jailbreak the device. Also, since you have an iPad2, your only option is to move to IOS6 as things stand today. You cannot restore any other version of IOS.
If you don't want to lose anything, all is not lost however. A full backup (using iTunes or iCloud, whichever you have configured on your iPad), will safeguard your app settings, media, etc.
So, the process you need to follow is...
1. Backup the device.
2. Restore to 6.0 using iTunes
3. Choose "Restore from Backup" when the process completes, and your app settings etc. will be restored, and following a full sync with iTunes, your device will have the same configuration as it had at step 1, but MINUS the jailbreak, tweaks, themes etc.
You should note, that if you choose to do this, you will lose your ability to jailbreak again for the time being until a new jailbreak is developed and released for IOS6. That may be many weeks yet. Nobody knows
Good luck.