Two cents chucked in the tollbooth of the writing life's slow lane.
Being true to the story is all that matters. If that makes readers squirm, then it's working at its highest levels. That's not to say that every story must evoke squirmage (moving readers for any reason is good), but to point out that the power of the story is in its truths. You start watering that down because of your perception of what may offend (notice that I said “perception”), then you damage what is strongest in the writing.
What are these truths? They're emotionl, psychological, and even philosophical, but that absolutely does not mean you have to belive them. You only have to make them true in the context of the story.
Now, have I muddied the water?
Here's an example. Write about a serial killer who believes that what he does is for the absolute good. No one in their right mind will agree with the bastard, but if you're going to be true to the story and that character, you're going to make him one absolutely convincing son of a bitch. If you don't, he's just going to be one more of those one-dimensional “he does it cause he's kuh-kuh-kray-z” villains we've all seen and depsise not becaue of their villainy, but because writing shallow is a copout. If you don't dig into that nutball to find out what makes him tick, and if you don't put it on the page, you're not doing your job.
Same thing with any other part of a story that may seemingly cause offense. Dig into it. Expose it.
Your heroic characters, if the exist, will duly counterpoint, and the squriming will subside.
(P.S. I'm the one in the slow lane, not you.

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