I wish. The email accounts let you pick what you want to sync up, but as far as I can tell Facebook doesn't.
I'm right there with you, I don't like the messages syncing with no option to disable it. I had like 100 old messages in my Facebook inbox that I had to go and delete, talk about annoying.
For me it's the chat/conversations that was taking the most inbox space in the message app (and consequentially the most annoyance). I didn't realize that the conversation format was turned off by default at the time.
Another thing, I have no messages that were actual "letter" messages showing up in the message app at all
I'll add my voice to those who would like to disable the messages for facebook. I chat with a lot of friends on facebook, and every single sentence shows up as a new message in my playbook inbox. It's extremely annoying.