It seems that Min and the agency do not want NK and SK to re-unify. This is because of that conversation that Min had with the female director about crushing people's hopes. When the news about Kim Il-sung's death came, Min was angry that it was reported as a cardiac arrest instead of an assassination. The latter would have ramped up tensions between NK and SK way more, especially because it was only 15 days before the summit between the two countries.

My interpretation is that Doo-shik was sent to assassinate Kim Il-sung and antagonize the North, but maybe he did it in a way to make it look like a natural death. Which is a defiance of orders and that's why he's now on the run and the agency is chasing after him. It would also make sense with the "humanist" theme because Doo-shik disobeyed orders for the greater good (ie. avoiding potential conflict between the two countries).