White lies are trivial, diplomatic, harmless and unimportant. You're making it out as if Jonathan is some kind of oracle which is just as nonsensical.
Like I said it's like someone saying "it'll be alright in the end". Just because something does turn out to be OK doesn't mean that what that someone said was meant to be initially taken as the foretelling of destiny. There's a name for this fallacy but it currently escapes me at the moment...
You also have to consider that his words are contradictory because he wants to give his son some hope and to leaven an otherwise depressing life lesson, otherwise all you get is this:
Jonathan: The worlds going to hate you if you reveal yourself because they'll generally be untrustworthy, misunderstanding and scared of you.... welp, it's dinner time, I'll see you inside.