He said:
"For those of you in the administration, who are coming after me ... remember, you've broken three [of the 10 Commandments], let's not make it four; thou shalt not kill."
What's the context?
Immedietely just reading that and only that, not reading a bunch of preconditioning media matters opinions or spin on it, and taking an objective look on it even ignoring who said it...i'd say its someone using hyperbole and allagory.
The only way I'd read that, from a purely objective point of view, as someone LITERALLY believing the president is going to literally kill them is if they didn't have a history of using allagory or hyperbole to make points and did have a history of being extremely paranoid or any legitimate reason to believe it to be true.
Commentators, regardless of their sign, tend to use heavy doses of sarcasm, hyperbole, allagory, and other type of devices to heighten their entertainment value and to put across their points. Beck, while definitely having some crazy ideas and views at times, does not seem to have provided any evidence that he's crazy enough to believe that the government is actually tying to LITERALLY kill him let alone state such on TV if it was legitimate, and I've seen no reason to believe such things are actually true to inspire such an idea.
That, mixed with the attempt at the theme with breaking commandments, it seems more an hyperbolic comment equating "kill" to "silence" so that he could slide another commandment break in there to complete the imagery.
This is also why I would say context would be important. Prior to the clip or leading into it was he discussing fears of the administration attempting to silence critics through various methods (be it direct or indirect) and thus when he talks about coming after him and "killing" him it'd make it even clearer that it was possibly simply alagory for silencing opposition.
But wait...
Media Matters gave extreme spin on their inteprirtation of it so that's naturally the only way to possibly interprit what was said. My bad, sorry...