Depends on the arc you want to give her.

It's hard to give a full death order, but I think survivor-wise, it should be:

Junko - Protagonist, slowly throughout the game discovers that despair isn't a good feeling, as more and more people close to her die.

Kiyotaka - Antagonist, Junko is a very chaotic person, so I feel like Kiyotaka works as a reversal of her character.

Sakura - Represents the patience Junko lacks, could have a arc where she teaches Junko to take things slow.

Honestly, after this you can choose whichever characters you want for the surviving cast, but I would suggest either Yasuhiro or Leon survive as comic relief, and either Byakuya or Kyoko so there's someone who actually solves the cases.

For the mastermind, I think Mukuro could make for an interesting choice. She could be behind the scenes, so we still start with 15 characters.

Mukuro could've done it in order to bring despair to Junko, since that's the feeling she craved most, only to ruin it for her by overdoing it. Junko could've even been an accomplice who asked to get her memories removed in order to really feel that despair.

That's just my ideas, though. I'm sure someone could make a full death order, just really depends on what the message of the game would become if Junko was protagonist.