1) "Additionally, we process words much faster than we process colors". Wrong, I'm pretty sure areas V2/V4 received information much faster than the visual word form area, especially given that it may require a saccade to take in a long word. Not sure where this claim comes from.
2) "...we instinctively jump to luminous or high contrast colors with our eyes, interrupting reading a program in a more standard way..." Half-true. There are well-known pop-out effects, but it's unlikely we read programs the way we read prose, so it's not clear it's an interruption at all.
3) "When syntax highlighting is on you also are spending cognitive energy (which is finite) on item-specific processing rather than organizational processing." No evidence offered. I could just as easily make the counter-claim, that syntax highlighting frees up the brain to more organizational processing, since there's less load necessary to figure out item-specific properties. Not necessarily wrong, but needs to be tested.
I think the biggest mistakes in the article (and perhaps what he got from talking with his friend in the cognitive sciences) are equating prose with code, and not accounting for novelty effects. I have no doubt that coloring random words in prose disrupts things, since it's novel and captures attention. But it doesn't automatically follow that people experienced with syntax highlighting experience similar effects.
It would be cool to see more actual research in this area.