Taibbi strongly insinuates in the article (and then confirms this was his intent in the comments) that the intelligence community is acting out against Trump because they do not like him, not because he is actually corrupt or because they have a duty beyond following the orders of a President.

That's a pretty strong accusation, and one he doesn't really present sufficient evidence to support here. He claims a "government-in-exile" situation without explaining who that benefits (who's in charge of the government-in-exile? Certainly not Clinton. Apparently not the Democratic party).

In essence, he appears to be buying into an illuminati-grade conspiracy that "they" don't want a Trump Presidency without a lot of support for why or how the alternative benefits them, which is irresponsible and sad coming from Taibbi. Especially since the simpler explanation - the guy with a history of corruption has done something corrupt - is at least as plausible and would necessitate the intelligence community to respond in some way (while still doing their damnedest to maintain their oaths of office in light of the Commander-in-Chief being someone they know is a crook).