Sorry, but you are wrong. Rivera even said that wasn't Godfrey's assignment. It was 100% on Thomas.
The coverage didn't look like 3-deep (cover 3) to me. It looked like cover 1 with man coverage underneath. Every CB appeared to be playing man to man - you can tell by the direction they turn, towards their man and not towards the QB. The LBs were also in man - I think they should have been blitzing. TD looks like he's spying RW, Beason looks like he has the TE (who successfully blocks CJ with no help - how does that happen?), and Keek has Lynch on the fake handoff.
Thomas took away inside leverage, essentially leaving himself on an island on the sideline. No way a FS can get to a deep sideline throw in cover 1. It was just a great play call for the defense, and great execution by RW and Kearse.
Thomas killed himself when he got too far behind in the trail. Have to be closer to the WR in man. See how Norman does the same technique but stays even with his man because he knows there's no help on the sideline. Munnerlyn loses inside leverage to the slot but he knows he has help in the middle.
If you are a CB, you don't complain about help over the top when you're in man. You blanket your man and don't allow him an opportunity to make a play. Though, I really think CJ should have put more pressure on RW with only a TE blocking him.