1. In principle, transaction fees can't be recovered. What's paid is paid, and since Bitcoin transactions are irreversible, you simply can't take back what you've already sent. What happened here is that F2pool created a separate transaction sending Paxos an amount that was deemed extra.
2. The mining pool or company that sent it back isn't necessarily good. We won't be thanking a god for it. It just so happened that they're an identifiable company that has a public reputation and that the company who committed the error was also a popular company. I doubt F2Pool would be good enough to consider sending you back your transaction fee if you erroneously paid $2,000 for a $10-transaction.
3. Paxos should learn its lessons. At the same time, we should also learn ours. Paxos had just inadvertently shown a huge red flag. We should be more careful in dealing with it. Paxos is a trust company and it shows it might not be worth our trust in handling funds.