It seems to me that this was a corporate coup with assistance from the prosecutors office. The plan was Ghosn would be arrested, admit guilt straightaway, possibly under some questionable interrogation[1] and then get a fine/suspended sentence. Nissan could be free from Ghosn with a minimum of fuss.
Of course, it didn't go down that way, but Ghosn fleeing the country was probably the next best thing. Public opinion in Japan generally seems to be "Why would you run if you are innocent?" and the case is forgotten.
It will be interesting to see if any revelations come out in Kelly's trial (currently underway).
[1] https://www.nytimes.com/2007/05/11/world/asia/11japan.html