Deciding who dies in a story

If storytelling were itself a story, the main conflict would be between two beasts: Freedom and Constraints.

When it comes to action, battles, duels, and combat, they all grant a boon to Freedom.  Because, honestly, you can write a combat scene to come out almost any way that you want.  Who wins or loses, who lives or dies, often has little to do with who is more powerful or who has the greater numbers.  The Constraints are instead provided by what makes story-sense.

Sometimes, what makes story-sense also makes physical sense.  For instance, it makes sense for the greenhorn protagonist to lose at the beginning of the story, not just because they are inexperienced, but also because it sets up further conflict.

On other occasions, what makes story sense is the opposite of what makes physical sense.  One example is the law of conservation of ninjutsu (look it up on tvtropes), where the strength of an army is inversely proportional to its size.  In a story, the strength of a character is often proportional to how much we care about them, and we simply don't care about large numbers of faceless individuals.

Other examples left as exercise to the reader: Why are love interests so frequently captured or killed?  Why is the protagonist's mentor always fated to die?  Why are the first ones to die in a horror film always the hot girl, black guy, and gay guy?

There are of course other means to add Constraints.  For instance, if you really wanted to be realistic, you could have the winners determined at random.  I would call this "aleatoric storytelling", named after aleatoric music.

From XKCD

For obvious reasons, aleatoric storytelling isn't very popular, except in sports and D&D.  You'd end up with a lot of things that don't make story-sense at all, like having the protagonist die or having them achieve victory at a random point in time.

Another way is to establish a set of rules about how your universe works.  This is the path followed by Death Note and HPMOR, for instance.  On the other hand, this is usually something a writer will attempt only if they think themselves clever enough to get around the constraints.  It seems you really need that Freedom.