If I delete an imessage from someone in IOS6, the moment i send them a new text/message, the entire chain of previous messages reappears.
There is no way to clear the history at present.
Apple didn't release an interface or tool to purge the messages that are stored on iCloud. You can only control and delete from the local cache of messages once they have been downloaded. Presumably they eventually get discarded, but there is no web interface or way to ask that the actual messages be deleted at the source. Nor is there a way to mark a message as to be deleted across all devices or in the cloud servers. Each deletion just deletes that message from the local cache of the machine doing the delete as opposed to permanently deleting anything.
See these threads for more details on this behavior:
I've confirmed this behavior with direct discussions with Apple Support in the summer of 2014 that deleting a message from one device won't actually delete it anywhere else or from the cloud store for your account.
Go to the "Messages" screen where it shows all the contacts you texted and select edit, then delete the entire conversation