"A game deserves the players it lures." personal and cherished quote of mine.
Existing counters
The duchy is supposed to ensure the security within its territories, at least against roaming bandits, raids and wanabee terrorists.
Pillages and war crimes are certainly a sure path towards negative affinities en masse, especially for the leaders and what they stand for... or are they?
While the royal charges (sheriff, judge), local enforcers, vigilantes and guards are supposed to deal with criminals. Some mafia and influencial organisations will probably provide implicit "protection" as well.
As usual, time and money as gateways
But most importantly, mass disruption of the intended gameplay will only occur if it is lucrative or free enough (both gamer-wise).
For elyrian characters to be effective, base skills need to be (re)trained, legal/mature be reached again (for developed attributes), trusted identities forged or worked to (carry permits)... which may take several out-of-game weeks every time.
Specific to Elyria, playable characters don't fade away on logout, fugitives still reachable against retribution and bounty hunters. Still a bit of a wild wide west vibe and romance, yet most troublemakers didn't live long or rich back then... being denied the comfort of sustainability and peace of mind (rest).
About getaways and hideouts, please refer to the next or the first point : duties of the duchy and the kingdom. As such expect (unchecked) crime rate to rise in time of wars.
Unusual dynasties
Family names and reputations are generally a boon, except when a member is tarnishing that name. Banishments will stop the bleeding but won't redeem the infamous stain so easily.
For sure, some few families won't police their members the same way, and will thrive on fear and mayhem instead. That's expected, this sub-game of cats and mouses.
Larger and it's called war, and elyrian battlefields have their own rules of engagement, not sure they have their own instances yet (to ease the game system, avoid collaterals and enjoy gamers' warfare).
Subtle nudges
Lets imagine for a minute that a negative affinity would cancel/reduce the usual protection against consecutive spirit loss... non-combat mob lynching hardened criminals could become quite the game-logic determent.
Negative affinity occuring when a player decides on abnormal gameplay relative to the character's tenets (depends on tribe, local laws... and plenty circumstances easily evalued by the story engine).
A typical Janoa, though wild hunter by nature, will imo gets such a penalty by killing a random-or-not cow in a field... you can't call that a hunt, more like spiting on the tribal totem.
So who else but deviant would go out of their way to cull the herd without a story-anchored reason (easing a mad/ill cow, avoiding surpopulation, as food for the owning family...)? Ah yeah avid gamers. ^^
Fear of death?
Petty theft may not incur death penalties but cold murder (or even attempt in some famous cases) in most medieval societies is a death sentence for both ends.
Especially since sparks of life would become a costly affair in unruly PvP, since they thankfully can't be "earned" in-game... or at most with story points (which are the opposite results of a destructive game experience).
Finally skill ramp-ups for that particular soul fade with each additional premature permadeath, and talent opportunities are also wasted. "Was it worth it?" is a very valid question when playing deviant characters in CoE.
Tainted origins?
Fair rules from the creators - and fairplay from the players - allow a game to stay fun after all.
That's the main difference with simple entertainment like (killing) arena, (freak or scare) show... where imbalance provides pleasure to the mass as long as their are not the challengers/victims/participants.
A careful design doesn't need to go far or convoluted to achieve a gravitational balance in a game.
Have a nice day, thanks for reading.