Hate to be the one (to mildly) come to the defense of this ridiculous article, which I stopped reading because it was so poor but which, after all the hysteria, I had to go back and read more. Much of the hysteric reaction against the piece illustrates many haven't read it. There have been, however, some very good point by point rebuttals and take-downs: there are all sorts of historical inaccuracies, generalized leaps, assumptions, etc. which are highly problematic. Gilley could have produced a far better article (he's been publishing in TWQ for over a decade) that critiqued research tendencies that have logical problems and that ignore evidence without dropping the mic after supposedly making "the case for colonialism" in this screed. But he seems to be in a burn it all down mood (see his APSA resignation letter). I'm still expecting him and editors from TWQ to say this was part of some kind of experiment.
But there are also kernels of truth in the article, and he does cite various mainstream research throughout (84 footnotes). The paragraph on p. 3 that discusses the "violation of epistemic virtues" is on the nose. Just one example: "Colonialism is credited with near-magical powers to sweep away everything good in its path (like tribal chiefs or ethnic identity) and with equally magical powers to make permanent everything bad in its path (like tribal chiefs or ethnic identity)."
Also, on page 5, it is ideas like this which tend to make many who ignore the political and economic mistakes of revered post-colonial leaders livid: "Anti-colonialism ravaged countries as nationalist elites mobilised illiterate populations with appeals to destroy the market economies, pluralistic and constitutional polities,and rational policy processes...." That was the case in too many places, and we see leaders like Mugabe still in that protest mindset, no matter the economic cost to Zimbabweans.
He could have made a case for rigor in studying the post-colonial political and economic track record without the reactionary normative stance in favor of colonialism. Getting this piece published in TWQ was designed for maximum reaction. Best response would be to ignore it, but now EVERYONE knows about this.