While there is nothing involving Sci-Fi or Fantasy in this scene, I am sure I read it in a Sci-Fi/Fantasy book. Probably written since 2000.
Good Guys (very militarized bunch) set up in a cover business in a city. (Don't remember what. But maybe like a dry cleaner, or restaurant, or warehouse.) I don't remember why they needed the cover.
After a few weeks they get approached by Mr. Bad Guy and a couple henchmen who want them to pay for "protection" or "fire insurance". Leader of the Good Guys group tells them we are not paying, and for his men to rough them up real good and toss them out the back.
Mr. Bad Guy says something like: Don't you know who I am? You can't touch me! And one of the henchmen confirms yeah he is our leader.
So the leader of the Good Guys group says OK, we won't touch you. Bust up the henchmen, and his guys start breaking their bones (Hands, arms, knees, legs, that kind of thing if I recall right) [Pretty sure they were only hospitalized and opposed to killing them] and tossing them all out the back door.
Mr. Bad Guy is pissed. He gets more members of his gang (6? or 7?), and they crash in trying to get payback. But the Good Guys group are not surprised, and ready for them. They grab them all and tell them: we can't touch Mr. Bad Guy, but we can touch you, and proceed to bust them all up except for Mr. Bad Guy and toss them all out the back door again.
Now Mr. Bad Guy is Really Pissed. He gets even more guys (a dozen?) with guns and they try again. But the Good Guys group (militarized, remember?) easily get the drop on them and capture them again. And once again tell them: Mr. Bad Guy says we cant touch him, but we can touch you, and once again start breaking bones and heads of the crew in the attack.
Mr. Bad Guy gets really mad and starts getting more of his gang together to attack again, and the gang decides they have had enough and kill Mr. Bad Guy and elect a new leader who decides they don't want any part of the Good Guys group.
At first I thought this was the scene from David Weber's "We Few" but upon reading it, see they just paid off/hired the gang. Then I though it was James P. Hogan's "Proteus Operation" But I see there the good guys went to the bad guy and killed him.