That's ridiculous. If they want to avoid trouble with CFTC the answer is to register with them, not some home cooked idea that segregated wallets would keep them clean. I simply can't believe that the CFTC would take a second look at their BitGo setup and say "sure, go ahead, no need to register anymore". I don't even believe that was the intention, it's wishful thinking in hindsight by the spectators over at Reddit.
Yeah, it would be stupid if it was the only action. As I understood, they paid 75kusd fine, then applied for the license as well, and did bunch of other compliance-actions. Segregated wallets were one of those.
The exact discussions/dealings between CFTC and bitfinex are of course unknown.
If bitfinex hadn't implemented the segregated accounts, they would probably be much better off. One reason for segregated accounts was speculated to be the CFTC trouble.