I just finished playing your game!
Man, what a great story! I enjoyed reading every bit of this one! also, the karma system was pretty neat too!
I think the next steps for you is focus on having a system built into the game to keep track of your points. You can just show them as points at the top of the screen or an actual bar for each side.
I did notice there was one time I was presented with a series of choices and a handful of them were red. (Pacifist run). When I clicked on one of those choices, the game crashed and said it couldn't find those choices. I had to playthrough the story again to catch up to where I left off.
Maybe you could add some sound in the background that sounds like a battlefield to help paint the picture better too!