Why would you conclude that? Based on that logic all 7 BTC from the first coinjoin belong to bob. There were two inputs to the same txn one of which (the 5 BTC txn) you know belongs to Bob. Thus both inputs and all the outputs belong to Bob. Right? Also this is a highly simplistic example. In reality a coinjoin transaction will involve many participants. Gmaxwell also points out in the coinjoin introduction that properly done it should involve multiple rounds. So Bob should take some of those coinjoin outputs and use them for another coinjoin transaction and those outputs and use them for another coinjoin transaction.
Also the naive solution is to use a centralized server but that isn't a requirement. It is like saying a system like Bitcoin need a centralized server to hold the ledger or that peer to peer file sharing still requires a centralized server for tracking. Making a centralized system is easier so they often come first but in time coinjoin will grow to have a decentralized peer finding capability as well. The peer setting up the transaction would still know the input/output mapping but using a two step commit and blinded output signing it would be possible to make even the organizing peer blind to the final transaction map. Combine that with multiple rounds and you have a very robust solution.
You point out the 'flaws' of decentralized trustless systems and forget the obvious. If I worked for a three letter agency and I mixers would make my job difficult in the future, I would be adovating now to either create or infiltrate centralized 'secure and private' mixer services to be honeypots for compromising privacy. It would make things very opaque from the outside but at the same time make things very transparent for those who have access to the logs. Provide me cryptographic proof that a mixer doesn't keep logs. Even a mixer started with the best intentions is subject to infiltration by coercion, bribery, and hacking. Last time I checked our friends in the three letter agencies are good at all three. This is why 'trust me security' is fundamentally flawed.