The scene Benioff was talking about is almost certainly
The Red Wedding
It was recently revealed that there is a casting call for cellists "ideally men with medieval or period faces (i.e. long hair and beards)", as well as "LEG ONLY, MALE AMPUTEES" who are "OK and comfortable with filming a scene within the context of a battle where your leg has been injured. Prosthetic makeup will be applied as though your leg has newly been severed."
The Cellists make it almost certainly the aforementioned event, as music was a key part (The Rains of Castamere, anyone?).
The scene itself is one of the most heart wrenching and emotionally disturbing in the entire series, and George R.R. Martin himself has stated that the scene is the most difficult he has ever written.
On a personal note:
The willingness of Martin to kill off of major characters has become one of the stand-out aspects of his writing, and the shock of realizing what has happened the first time I read it really changed my perspective on the whole series, even more so than the death of Ned Stark.
Regarding the full context of the interview with Benioff referenced in the question:
The Red Wedding seems particularly suited towards an incredibly momentous and dramatic televised scene, largely due to the tension of the wedding leading up to it, and the fact that the combat noises are drowned out by loud music. I can easily envision bloody fight scenes interspaced with dramatic closeups of musicians furiously playing as loudly as they can, and this ties in almost exactly with the casting call descriptions cited above.
Regarding the second scene mentioned, I can only speculate. However, in addition to the other scene you mentioned in your question (which does seem a very likely candidate), I think these are just as likely, if not more:
Daenerys taking command of the army of Unsullied and turning them upon their Astaporian masters, the duel of Oberyn Martel vs. Ser Gregor Clagane, the escape of Tyrion, or possibly even the return of Catelyn Stark.