There's no reason why you can't have an effective midfield two that can stop the ball being played through them - the classic example is Viera and Petit - but Alonso and Gerrard simply aren't the type players that can provide that type of defensive security.
Interesting post, and some very good points on the tactical side of things.
However, I think you're falling into the trap that a lot of people are - namely, that of judging Alonso and Gerrard on this one game, where they weren't at their best and slightly overrun.
You need to remember that Alonso made the 2nd-highest number of successful tackles in the Premiership last season. He provides a lot of defensive security, so I don't buy your comment. Gerrard is also a hugely effective defensive player, even if he's not someone to simply sit and hold. His covering back and tackling is superb. He just left a few gaps on Saturday, and sometimes you have to take risks.
It's also important to point out that Gerrard and Alonso, as a midfield two (in a 4-4-2 formation), were by far and away the best central pairing at the club last season. When they played together centrally, the Reds scored more goals, conceded fewer, and won at a rate of nearly 2.50 points per game (compared to the overall league rate of 2.14 points per game). Sissoko was (and still is) a very important player, and a brilliant defensive player, but Gerrard and Alonso guaranteed far better results last season than any other pairing, and were also good on the defensive numbers, too. As an individual, it was also Gerrard's most productive position - better for him than as a 2nd-striker or on the right wing.
I don't think defending like a Martin O'Neill or Gerard Houllier team is what we should be pining for. Benitez's side last season was harder to break down than any team those two managers has ever had, and this season we needed more creativity and pace going forward, width, and some new striking options, which we now have.
But it might mean being a little less solid. So long as the wide men tuck in when we don't have the ball, and get wide when we do have it, it's not going to be a massive problem; it's the risk you have to take to move onwards. It's also true that Carragher and Riise were the two most reliable defenders last season, and with half the regular back four missing we're hardly going to be firing on all defensive cylinders, so that can't be judged. It will take Aurelio time to adjust, just as it will take players like Pennant and Gonzalez time to understand how Benitez wants them to play when we don't have the ball. Agger, meanwhile, is an amazing prospect but he's not yet in Carragher's class regarding reliability, nor does he have the defensive leadership.
Were it not for a couple of exceptional strikes from Gerrard - as well an assist - it would have almost certainly have been the team from East London lifting the FA Cup rather than the one from Merseyside.
Again, sorry but this is the same dodgy logic written about Agger's goal - that we shouldn't be relying on great goals, and if it wasn't for such goals, etc, etc.
The fact is that's what Steven Gerrard does. That's why we pay him £100k a week (or whatever it is). Crouch had a good goal ruled out, and West Ham only led 3-2 thanks to a wayward cross, so as well as West Ham played at Cardiff we can look at a lot of different events in the game rather than just say "if Gerrard hadn't done this or that, we'd have lost".