The full graphs at the end of the report are interesting, thanks for the link. It's difficult without more detail on the "Flight Path Analysis" to draw firm conclusions: it may be that the AOA trace was inferred using some fairly weak assumptions -- it's not from the flight recorder.
I don't think we'll ever know with certainty what happened. The CAB cites the interaction of vertical gusts with control inputs. I find it difficult to see how the vertical gusts could in themselves cause the pitch-up in a way that is consistent with the data. I can certainly see that they could cause confusion and control inputs that made matters worse.
If the aircraft were to encounter a strong downdraft, a pitch-up would be accompanied by a spike of downwards acceleration, until the AOA recovered to its trimmed value. The excursions between 7:00 and 11:00 in the trace show that sort of effect.
You can argue that there's some evidence of that in the traces around 12:05 (though the acceleration never falls below 1g), but you can easily also argue that it was in response to a control input, as has been inferred in the elevator and stick force traces. Between 12:05 and 12:10 there seems to be a nose up control input, and if the aircraft was already above its trimmed airspeed, that's only going to make matters worse.
The pitch-up seems to be a combination of being above trimmed airspeed (whether or not I can persuade you that that was due to a horizontal gust), and a nose-up control input. There's little evidence that it was caused by a downdraft. Regardless of the cause of the pitch-up, what broke the aircraft was the irrecoverable dive induced by the subsequent sustained full nose-down control input.
To address wsherif1's original point, I think the CAB does at least speculate (page 42) on why the nose-down input was held for so long -- a combination of the negative g (perhaps they couldn't even reach the controls?) and the lightening or reversal of stick force at high down-elevator loads on the 720.