News to me is that *all* your coins are at risk. I thought it was just clumps of coins (previously received transactions) involved in the transaction, not my aggregate balance. Yikes.
You were right before. The reason all of his coins were lost is that he first transfered all ฿9000 to himself, merging them into a single TxIn. If he had skipped that step and gone straight to sending himself ฿1, he would have only lost the smallest payment that he had previously received that was over ฿1.
I think the client needs to communicate TxIns and TxOuts better to the user. I don't know how to do that without being confusing, but there are real privacy, safety, and security implications in which coins the client chooses to transfer.