Hmm. Two thoughts. Posting thought bubbles is not metagaming. Metagaming is using outside (or personal) knowledge that the character does not have in-game. Thought bubbles don't cause metagaming, they just provide extra opportunities for it.
I think the risk that someone might use knowledge of my character's thoughts for metagaming is worth it considering the gain that can be had from everyone, not just the DM, getting an insight into what my character is really like.
We have a hard enough time roleplaying a "character" in person, what with all of us being repressed, minnesotan, non-actors. Doing so in written form is doubly hard. Thought bubbles help.