[halfthishalfthat]

The simple answer is just "you don't use に here".

But maybe it will help you to think of に as denoting kind of a "target" for an action/verb, and you don't ... die toward malnutrition or something like that...

But even after reading what I just wrote I don't really think it can sum up all the differences between the two since they are just... really extremely different.

Here で is showing you the manner/method/reason for dying.
Since you die from/of malnutrition or because of your malnutrition.

It's not just constricted to "by (means of)", but this translation of で can be pretty encompassing I think.