There is absolutely no way anyone could have caught that ball. Watch the replays, they would have had to jump ~20' into the air! Grounding was the correct call, he airmailed it to avoid the safety by Tuck (ironically).
Any penalty that occurs behind the GL gets a safety. It's rare to be sure, but happens a few times every season, at least. I see no issue with the rule as it stands. It's in place specifically to prevent what Brady did.
The D can get a penalty that will award the offense a TD, it's just extremely rare. They fall under the jurisdiction of the palpably unfair act (now THAT'S an obscure rule!!). A good example (yet still a non-call) would be the Jets coach tripping the Miami returner. AFAIK it's never been called in a game, though.