Of course, the two narratives don't have to contradict each other. It's possible that large numbers of Yemenite Jews wanted to reach Israel, for multiple reasons, and that the complicated task of extricating them and bringing them to Israel was woefully mismanaged. Woeful mismanagement is, sadly, a very common condition.
Past and future researchers wishing to work out additional perspectives of the question will find lots of relevant documentation here at the ISA. This blog won't try to argue either case, preferring to present a single document created by someone who didn't know about the historical interpretations because he was busy being there at the time: The report of Dr. Moschytz, a physician sent to Aden in the second half of October 1949 by the ministry of immigration:
First stage: the escape from Yemen is not coordinated at all, prior to the arrival of the people at the border of Aden. I'm not aware of anyone directing this escape. In any case, we heard rumours of an additional 15-18,000 people on their way to the border, and we have no idea if they're rich or poor, if healthy or ill. The last time that Hashed [the transit camp in Aden] reached a capacity of 13,000, the border was sealed for a month, and some 4,500 people accumulated beyond the border. They all contracted malaria while waiting; many were left totally bereft. The JDC sent medicine, but many of them refused to take it. At one point the JDC supplies were sufficient but at a second place it wasn't, and some of the people died of hunger.
Second stage: En route many of the locals assist the immigrants for high fees, so that they arrive penniless. Their physical condition is awful, and the children suffer the most. It's no surprise that the mortality rate is high, mostly from sickness but in some cases from hunger.
Third stage: the camp gets a warning of a few hours that new people are about to arrive. Before the camp learned how to deal with them, desperately ill people simply died where they were put, because they had never seen a doctor before, and the medical staff didn't know to seek them out. Now they're brought to the hospital and given medications against tropical fever. Many of those who arrived at death's door leave the hospital as soon as their fever goes down, falsely believing they've been cured and desperate not to miss the plane [to Israel]. The hospital staff had to build a fence around the hospital to prevent the patients from escaping in this manner...