I was running a one shot for friends and a player had gotten annoyed with an NPC that the other players really liked. This came to a head when after a combat encounter the Player decided to attack the NPC with the intention of killing them. I let one of the other players take the attack as a reaction but the attacking player was clearly very annoyed and I felt like a complete jerk.

I would've preferred for this to not have happened. I think the other players would've preferred it not to happen as well. The attacking player later explained that they felt the NPC was being a distraction and that they felt they needed to get rid of the distraction.

Is there a better way to deal with this situation in the future without being a jerk?

You were not being a jerk

Both of your players were offered agency: the one got the chance to attack an NPC and the other got the chance to interfere with a murder.

If the murder hobo player is upset about this, what you next do is discuss with them why they feel that way, and why they feel that killing NPC's out of hand is a solution to any problem when the other members of the party do not.

What if this comes up again?

Death saving throws for NPC's in within your remit as the DM to use.

Monsters and Death

Most DMs have a monster die the instant it drops to 0 hit points, rather than having it fall unconscious and make death saving throws.

Mighty villains and special nonplayer characters are common exceptions; the DM might have them fall unconscious and follow the same rules as player characters. (Basic Rules, p. 79)

You can use this for any NPC, not only "special ones," as the situation fits. This way the player could kill an NPC (well, drop them to 0 HP) but that still gives the other players a chance to try and stabalize/heal the downed NPC if their PCs are against this.

Experience as a player

About a month ago, my life cleric did this very thing when a few of the other PCs (my brother is the DM) got carried away with an argument with the town guards and ended up dropping three of them to 0 HP. I did my best to stabilize / heal them, and the DM went along with it based on the above rule. It worked out in the end for two of them, but the third one had taken "massive damage" so I convinced the other PCs (my nephew's rogue/ranger backed my play) to pay the widow a weregild. That happened during the next play session.

RP wise, it made for a neat session. Story wise, it turned out that people across the river heard of our attempts to make amends and it resulted in making more contacts, etc, with NPCs.

Experience with this as DM

The party encountered some hobgoblins mounted on Dire Wolves who did not attack, but approached the party. The party simply attacked them anyway. The last HG tried to surrender but the party wizard zapped him with a firebolt.

So I had him make death saving throws. He passed. When the rogue went to loot the hobgoblin I let him know "this one's still alive; unconscious but stable." He chose to ask the cleric to heal the hobgoblin. With a revived hobgoblin, they had a discussion about the real threat in the area: ogres, zombies, and ogre zombies. (Led by a wight). Those monsters had been a problem for the hobgoblin village a bit further north. They ended up letting the hobgoblin go home. (I now jokingly refer to the wizard as Quickdraw).

Change behavior using consequences

Consequences for villainous behavior

Ensure that the world you're describing has a reaction to the parties actions. Make it clear that the world they are participating in does not like nor want some kinds of behavior.

A party that gains a reputation as being murderous, might attract the bounties or end up as the target of good adventurers. This can be expressed through the subsequent interactions with PCs. Some examples that are usually pretty clear, but not debilitating are:

• NPCs that tell the party they've heard of them and are afraid of them.


• NPCs that will not help the party because of something specific they did and there is now a story about.


• Being hunted by a group of adventurers that have been tasked with hunting down "villains"


• Being refused admission to places or being asked to leave when they are recognized.

Benefits for NPCs dealt with nicely.

Make rewards for the kind of behavior that the world likes be tangible and tied to the behavior. Trading fairly, good deeds, and mercy could be examples of behavior that others will hear of and appreciate. An example is not slaying defeated foes.

Letting opponents live

Make note of opponents that were defeated and allowed to live or escape. Make the circumstances of that come back around. If the player characters were benevolent or malicious, that information will spread. Perhaps they encounter the relatives, friends, or allies of an enemy they allowed to surrender. The treatment of the previous encounter should affect the subsequent interactions.

Figure out how to make the NPC less distracting

The other two answers are great, but as described it sounds like a social problem bleeding into the game.

• 
  

  Your player is frustrated and no one else seems to notice or care.
  The game gives them agency that they don't have socially, so they
  used what they had to remove their frustration.

  
  
  

  Without knowing more about the details of the game session, the best solution is probably to ask the frustrated player, then the whole table, how to resolve the issue.

  
  

In-game, I think you handled it right. The other players should have a choice in at least attempting to stop NPC murder. But it sounds like there is a root cause that needs investigation.

As general advice for not making your NPCs targets for murder:

• NPCs need to be useful. An NPC who isn't pulling their weight is luggage, not a person.


• NPCs can't be too useful. Assistance doesn't mean doing things for the players. Especially in combat. Combat NPCs should fill a missing role, and never outshine a player in their established role.


• 
  The players are the decision makers. Hopefully your rescued prince, despite being royalty, knows when to shut up and let the professional adventurers decide how to escape the bad situation.


• Murder has consequences. There should be in-game motivations for characters to not murder someone, even if they want that someone to die.


• NPCs shouldn't be complicated. Player Characters have a lot of stats and features. It's already a full time job managing the world and monsters, don't slow things down with a character complex enough to be someone's full time job.

I've recently come across issues with my players finding NPCs bothersome.

Regarding reason #1, in The Sunless Citadel, the first adventure in Tales from the Yawning Portal, there party has a chance to rescue a gnome captured by goblins, who can choose to accompany the players.

This gnome isn't a full player character, and isn't very tough, so I'd play him as keeping back and only taking a stab at enemies with a borrowed dagger when absolutely necessary. He can heal (like a L2 Cleric), but with limited spell slots he often came off as useless. He didn't really earn his keep until he saved a downed player character by dragging them out of combat before casting a healing spell, and even then the players (well, one specifically) only begrudgingly accepted his presence.

For my final point, in our most recent dungeon I introduced basically a GMPC that I intended mostly to be that other adventurer that happens to be adventuring in the same place at the same time as the party, that they could bump into here and there but would stay out of each other's way. When half of the group couldn't make it to a recent session, I brought this NPC as an ally to round out the group and give them confidence.

I unfortunately made them rather complicated, and had to take extra table time during combat to check class features and look up a couple of spells. Though the players were grateful for the help in combat, I could see in their expressions that they would have preferred things to be moving faster. I haven't yet solved this for myself, but being aware of the problem will make it easier to avoid this issue in the future.

Please see other questions about GMPCs as explanation for item #2, railroading for item #3, and the other great answers for #4.