I'm not sure why anyone is surprised about anything here. Of course NBC is going to try to do a hatchet job on Jones, they obviously want to protect their reputation as a trust-worthy news source. Alex Jones, as everyone knows, is a crazy conspiracy person, mainly popular with teenagers and senile old people. His lawyers stated during his divorce trial that he considers himself playing a character,
as we all saw in the Joe Rogan interview. Basically, Jones detests the hypocrisy of the media, which we saw plainly in evidence in the Megyn Kelly interview: certain subjects are off-topic, others can only be broached with the appropriate moral spin and so on. The mainstream media, which is entirely owned by a few huge multinational companies, clearly has its monopoly on truth to defend. Since Jones runs a shoe-string operation not unlike other outrage media (The Young Turks is the first example that comes to mind), he's essentially just spewing whatever he knows will get ratings. Sometimes he goes to far and gets sued or divorced or is forced to issue a retraction. The fact that media demonizes him really says it all about their concern for their own status as truth-speakers.
That said, Megyn Kelly is correct to point out that Jones has made shit up and is basically a snake-oil salesmen. 1776!