I think your statement could be better informed. The article you link to for example doesn't deny the common structure of cortical columns, but posits that they don't have a known function. That's kinda the point of Numenta's research. To suggest a function.
And it's not that the idea of cortical columns (or more specifically minicolumns) was found to be wrong, we've gone from a simplistic explanation to a more complex one via both more careful measurement, new techniques, and cross species comparisons. I think this review is pretty good on these points:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820381/
There's also this idea that the neocortex is composed of 6 layers. That idea isn't totally wrong but it's required updating as we gain more information.
Even the neuron hypothesis itself has had to undergo significant revision as we better understand the computational power of sub-neuron units and companion cells like astrocytes.
So if you want to criticize cortical columns for being an over simplification, that's fine, but 1. we all know that and 2. simplifications are particularly useful when you need to reduce such systems to code as the OP has done.