I hate to be a stickler, but:
The jet was only on the westernmost edge of the SAA during the early part of the flight - and negotiated this region successfully…
The jet was completely outside the SAA (and had been for some time before it went down).
Thousands of jets traverse the region every week.
In short - complete and utter bullpuckey.
A link is appreciated so that everyone knows which column you’re talking about.
Are you saying that the SAA was a factor? Because Cecil says it wasn’t.
No - I;m saying that the column does not discount completely the theory - it sits on the fence. Saying that 'part of the plane’s route was through the SAA" is disingenuous, since the route merely skirted the edge of said anomaly - and did so for a very short period of time.
AND the actual crash was nowhere near the SAA. It was hundreds of miles north of it.
So I am saying that the debunking did not go nearly far enough. The reply should have made clear that all of the evidence points to the SAA having nothing whatsoever to do with the crash 0 or any other problems, since thousands of planes and ships traverse it weekly.
We get a lot of comments on columns that are old, so it just makes it easier if there’s a link in the thread. 
As for your criticism, I agree. While the SAA is a real phenomenon (unlike, say the Bermuda Triangle) that has affected some machines, its causing the crash is highly unlikely. (I say ‘highly unlikely’ and don’t discount it completely because I don’t know enough about it, nor much specific about FBW systems.) Given the reasons you posted, especially that thousands of aircraft transverse the area without incident, I think Cecil should have stated flatly that SAA had nothing to do with the crash.
But the problem is without proof as to what exactly caused the incident, Cecil did not feel like it was honest to state authoritatively the SAA had nothing whatsoever to do with the incident. Perhaps he did not state as strongly as we might like that it was highly unlikely to have had anything to do with it (and I know from my discussing this with him that he does think it’s very, very highly unlikely), but it also wouldn’t be factual to state it was impossible for the SAA to be a factor.
I accept that, and stated that as a reason I said ‘highly unlikely’. But given that there is overwhelming evidence that the crash was weather-related, I think that it’s safe to say that while not impossible that the SAA might possibly play some role in aircraft crashes, it can be ruled out in this case.
Of course I’ve posted elsewhere for other crashes that we need to wait for the official report of an investigation.
I will link to the column I am discussing from now on. Sounds like a good idea - current column or not. 
I was just hoping for a bit more dismissal of the SAA ‘theory’. Just precisely how, a WEAKENING of the magnetic field could somehow disrupt onboard instruments (or interfere with their communication with orbiting satellites) is completely beyond me. Now - if the region exhibited radically STRONGER fields - or SHIFTING fields, that might be worth discussing. Even if the strength of Earth’s magnetic field is so abysmally low that a simple pocket magnet can overcome it easily.
But to leave the question ‘open’ is, to my mind, a shirking of ones responsibility to shoot down such errant silliness right up front.
It’s not the magnetism that causes problems with space vehicle that pass through the region, it’s the increase in solar/cosmic radiation which makes it through that portion of the radiation belts because the magnetic field is weaker.
To what extent that would allow increased space radiation to penetrate to the level of aircraft flight, and to impact aircraft electronics to the point of endangering the flight, is the main issue of controversy. As far as I can find, there is only a very minute chance of that happening.
Overall the one thing which is indisputable is that at this point in time, the reason for the crash of Flight 447 is a mystery and does not fall neatly into any one, specific conventional explanation.
Fyi, as Una alluded to, the only thing the magnetic field affects in an aircraft is the magnetic compass, which, these days, is more of a back-up instrument, and not even tied into any aircraft systems.
The way I read the column, Cecil was not on the fence; he seemed to be discounting the SAA notion but leaving a little ‘just-in-case’ wiggle room. You never know what little factors contributed to the chain of events that led to the crash–the first little link often appears a long time before the crash. If they skirted the area and around that time something started to slowly degrade in the aircraft’s computer system, and that led to readings the pilots and autopilot didn’t understand, then they hit severe turbulence with a degraded system they were in the middle of troubleshooting… then you can’t rule out the SAA as a factor. You just never know until you get the black box, and even then you don’t always get all the answers.