The insane suicidal being refered as "God killing himself" is of course the supreme being Azathot, which disembowelled corpse make appear a Nature/Fecondity female deity (obviously Shub-Niggurath), who manage to impregnate herself with the corpse's semen, then immediately give birth to a (physically grown-up) son. They eventually are beaten to death (and Shub-Niggurath is raped) by the cultists who shot the movie.
So, Begotten is actually a Snuff Film shot by some prehistorical primitive cultists during some blasphemous ritual, which involved some gruesome action against two superior beings. Don't worry, Azathot and Shub-Niggurath eventually got better, but considering how they were treated by our Prehistory ancestors, it isn't very surprising that Great Old Ones aren' very fond of humanity.
An alternate explaination is that the whole action is actually consented by Azathot and Shub-Niggurath, the movie being considered as Slapstick comedy by Azathot's court.