What I want is a way to disable Facebook messages from showing up in native messages. I hate getting emails for every line I am chatting in the Facebook chat in the Facebook client.
I may be mistaken, but I don't think the OP is referring to the native Facebook client, but rather the Facebook messages that are recognized as a new "message" in the Messages application.
I've found it extremely buggy and makes the unread count for new messages pretty much useless. It serves horribly as a chat application for Facebook as well, considering the lag time incurred when reading / sending a chat message.
I've just removed Facebook account integration entirely until I can selectively remove it from the Messages app.
I did change the settings from individual messages to "conversation" mode. It helped a bit. I'll try this for a few days but if it's still buggy I'll have to do what you did.