It does take two transactions to set up and teardown a payment channel. However, payment channels themselves have expiration dates, and once the channel times out your funds will be released to you. While a payment channel is active your funds are secure, but you cannot spend the amount you've staked to open the payment channel until you close it.

Now, say I move 0.1 BTC into the lightning network and I do lots and lots of microtransactions there. When the channel times out, the transaction cost for closing the channel is like 0.2 BTC. What will happen?

(this is an honest question - I haven't read the white paper, I don't know the answer to this).