Jonghyun's soul doesn't come back up. He only gets bottled up and released again. I guess you didn't get that opening The Gate leads to Heaven or Hell, or wherever the souls are deemed to go. Jonghyun's soul doesn't go into a Gate since he gets 'reborn' as another person or being everytime he 'dies'.

In my opinion, for the gravity of the crime Jonghyun committed, he's extremely lucky he didn't get Uncreated. Imagine if one of the souls Jonghyun didn't pick up on the day he decided to leave were the souls of Hitler, Caligula, Stalin, Idi Amin (of course assuming that time is a fluid motion in this example) can you imagine how earth would be?
Their job offers no room for mistakes or flights of fancy, because each Angel is indirectly responsible for millions of lives, even if they pick up only a handful of souls each time they go.