Only way I can justify it: Mephisto is a prime evil. Lilith a lesser evil. Both clearly already have influence over the entire party. Mephisto manipulating the hero into imprisoning him has to be part of his game plan.
Killing Lilith and imprisoning Mephisto is really the only logical choice. You were really going to side with a Lesser Evil, the daughter of Hatred, and think it was going to be all dandy candy?
I have no reason why they would let a child walk around with a prime evil soulstone though lmao.
For shako being the rarest item in the game, it's so utterly boring.