I agree with you that it was jarring but I felt that worked with the film since itself (the topic) is very jarring. The death of a child, the warring between nature and nurture, war of within with O'Brain and then his son; I feels like a movie like that demands a level of jarring or uneasiness because of the subject it is dealing with.
I wholly agree with what you said on your second paragraph.
I'm understand, with Malick you expect a film, something that defies the ordinary conventions and narration. New World ins fantastic but the only problem was Colin Farrell.