If it bugs you so much, try thinking of it as metaphor, not mysticism. All kinds of crafts rely on metaphorical thinking… reflect on the way we use geographic terms like “field” and “area” and “sector” in talking about ideas, or (more pertinently) how sociologists and political scientists use language that ascribes identity, intention, and other personal qualities to groups of people.
There’s no literal substitute for those metaphors that doesn’t lose the reality of emergent properties that affect the real world. Yes, we know that a nation doesn’t have literal identity or intention, and there are times when it’s crucial to remind ourselves of that – and other times when doing so would cripple the best mental models we have for understanding why all these individuals are acting the way they do.
Not all writers use the same toolkit or conceive of their work in the same way. I don’t naturally tend to think (even metaphorically) of my characters as people I’m discovering rather than creating – but based on my experiences of having to rework a passage until it fit the character, I can certainly understand the metaphor and its power.
I’m not going to tell writers for whom that experience is stronger and more central that they’re wrong to describe it with the metaphor of living characters, or that anything would be gained if they confined themselves to only speak in literalisms. Intuitive (not just “mystical”) phenomena are usually poorly served by literal-analytical language, and this is no exception.