Emotions are always complicated, the lines are always blurry, and the colours of the moral compass are forever grey.
Witchers are supposed to be neutral for some reason(to avoid being considered a threat to humans and their schemes and affairs?) never to meddle in the business of humans or factions, yet they choose themselves. Geralt chooses for himself.
Witcher are mutants and considered thus, yet there are persons from all kind of the fence(elves/humans,pro/anti some cause) that tries to get Geralt over to their side. They try to appeal to his 'human' or 'non-human' side, to his good and better senses, or outright command him to do their bidding. The 'lesser evil' speech. The most important things I got from Witcher universe is that monsters aren't always monstrous(no more than humans at least), and humans are mostly the worst creatures out there. Anyone remember Nivellen from Last Wish? Geralt was adamant that he wasn't a monster and he sure wasn't.
But what we're talking about here is rumours or reputation. People's opinions of what witcher are, not the truth of it. Ever stumbled upon 'The Witchman' entry in Bestiary journal?
"A witchman is by some called a witcher. Summoning him is dangerous, yet he must be called at times. When none can stand against an accursed monster, a witchman will. Do not touch the witchman, for you will become mangy. Remember also to hide the lasses from him, for the witchman is lecherous beyond imagination. Though the witchman craves silver, never pay him more than the following: a silver penny for a drowner, two silver pennies for a werecat, four silver pennies for a vampire."
As well as: "Witchmen roam the roads where monsters live; they spend winters in their keeps, where they plot and perfect their swordsmanship. Witchmen never get ill and tend to be resistant to venoms and charms, for they are themselves enchanted beings. They run from the sound of church bells; their greed for women is only surpassed by their greed for silver. A witchman is a master of the sword and sinister sinister spells. They are skilled alchemists, they create potions that make their eyes glow in the dark."
Some things are true, potions, swordsmanship, and witchers residing in a keep during winter months and so on, but even more aren't true.
My opinion? Witchers, though mutated, still have human emotions and they all have to deal with the troubles that comes with that aspect. Being better, faster and more resilient than normal humans does not account for much when you're still unsure of who's your enemy or ally, and when the 'right thing to do' isn't that straightforward. And it usually isn't.