Even better, killing him will send North Korea into disarray, in that time launch strategic air strikes to their military poi that possesses the highest potential threat to the surrounding areas.

And how are you supposed to just kill him? The US doesn't have a Death Note, they'd have to launch a military operation.

They already know that. A lot of North Koreans are already aware that South Korea is more advanced than them, and they are also aware that China is too. It's impossible to keep them completely shut out from outside information. However, the thing is, they were born and grew up in North Korea, North Korea is what they know and what they're used to, unless there's something extremely drastic that forces them to flee, their fear of punishment or of the unknown is going to keep the status quo.

Well... Yeah.

Which would mean the deaths of untold numbers of innocent people.

The trajectory of the missile was probably identified so Japan knew it was not going to land on it's territory. So perhaps it's better to just let it fall into the ocean to avoid spending millions or billions of yen on activating missile defence and possible political backlash. It also does make North Korea appearing as an aggressor on the international stage too which works in favour of Japan and it's allies.

And North Korea having nukes is the better option?

When they haven't used them to kill millions of innocent people, yes.

Because they don't have them. They are shooting missiles over Japan though.

If they really wanted to hit Japan, they'd hit Japan.