I completely understand your problem, for similar reasons, but would suggest "make the world fit your plan" and not vice versa.
My (fledgling) campaign is run on similar precepts, so I'd suggest considering a few points about a "realistic" setting:
The State is Epic Level
If there's a real dynamic to your campaign, then unless the "Mafia" is running the show on a national scale, there is organised law as well as organised crime. People in power don't like "murder" - mortality is their only real threat - so they are unlikely to be overjoyed it if people who are doing good acts are wantonly cut down in the streets.
And even if you live in a LE tyranny, vulgar displays of power from the criminal elite are unlikely to impress the ruling strata of criminals. And they can call on thousands of people, low and high level alike, to show the Mafia who's really in charge. This means that rather than getting his hands dirty and running afoul of the state, your crimelord may consider a few other options. Especially because...
NPCs Don't Know Levels
Sure the Mafia character is levels above the PCs, but he doesn't know that. All he knows is that there are a group of troublemakers who have caused him grief.
Could he best the Fighter in a bar-room brawl? Maybe not. Could he resist the Wizard's enchantments? He's not sure! Does he want to kill the Cleric and risk angering a priesthood or a deity? Not so much. Do they have a powerful patron behind them? They could work for anybody, maybe someone more powerful than him!
Most people who climb the ranks of the world do so by cleverness and politicking, so he might refrain from a direct attack because he wants to suss out whether it's worth pursuing them. Speaking of which...
"Real" People are Risk-Averse
Your Mafia boss doesn't know the PCs inside-out and isn't sure if he should take them on until he's done his homework. What should he do in the mean-time?
- Send A Warning: send a minion and some henchmen to gently advise the characters that their behaviour is problematic, and if they continue along the path they're following, there will be repercussions.
- Do Some Research: employ someone or something to check out the characters, find out how powerful they are first, and if they have any weaknesses; he may even see if he can work with them on some level (if there are Chaotic, Neutral, or Evil elements), rather than a mutually destructive conflict - think Win-Win, in modern business jargon
- Run Interference: send someone to infiltrate and lead the PCs off-track to remove the problem without bloodshed, insult, or unwanted attention. Maybe the agent could even take them into danger so the Mafia kingpin cannot be implicated in their deaths (hence avoiding all personal blame in the matter).
"Getting someone else to do the dirty work" is popular with powerful people for a reason. Why risk injury or loss of personal resources from a direct confrontation when you can send someone else and have absolutely zero risk of being damaged or implicated in any wrongdoing by legal or moral authorities?
"I've Got Bigger Fish To Fry"
Yes, the PCs have caught the Mafia Rogue 9's attention, but maybe he's got his own problems in your game-world? Perhaps the F/4 sheriff has called in some powerful bounty hunters who are sniffing around. Or maybe the PCs' activities have shown an upstart Rogue 6 in The Organisation that his boss has weaknesses that are open to exploitation.
Suddenly, your villain is too busy consolidating his own political power within the Mafia to deal with some upstart strangers who will probably only leave town in 2 weeks anyway? Basically, make something happen behind the scenes that occupies the powerful NPC's attention for the moment.
All people in "real" hierarchies are typically concerned with the people directly above them, directly below them, and competing at their relative level. Your world should be no different!
Plus, if your Mafia boss is in any way shrewd at politicking, this may lead to a "two-birds-one-stone" situation where he sets an ambitious but lower-power rival off against the PCs instead. Either way, he comes out with one less enemy!
I hope my suggestions are of some use!