Did I overstep the players' agency by forcefully resolving conflict they could have resolved by themselves?
Well, yes, in a way. Their agency was taken away by line of command by some authority figure. However, this wasn't a magic spell by the gods. Players had to agree to play in this command structure. All other players obeyed the command structure. If your character is a private in the army, complaining that the Sergeant, Lieutenant, Captain, Major and General all take away their agency is a little hypocritical. That is what the Army is and they agreed or even chose to play a private. And if every available character in the game is part of the command structure, at least they chose to play this game with it's constraints.
However
Regardless of whether this conflict resolution was better than an alternative solution, it might make sense to take a step back and ask: why the conflict in the first place? Wouldn't the best solution here be to not have a conflict of this scale? From your description, it didn't seem like any of you enjoyed it.
While it may have been a simple case of My guy syndrome, you didn't make any mention of an in game or in character reason that they had. Other than "those ******* damaged the ship".
You tagged this system-agnostic so it's hard to be sure and examples might be all over the place, but it does go for all systems I have played:
Personally, and I have seen that in others, so I'm pretty sure it's not just my little character fault, I get stubborn and conflict-happy when my character gets hit by the adventure in unrepairable ways.
When I play the game and something normal and by the book happens, lets say a critical was rolled against my character and something bad happens as a result, then that is just part of the game. And the game has way to handle this. Maybe heal spells. Maybe cyber limbs. Maybe the reward is big enough to buy another of whatever was lost. Maybe the tomb contains a flaming-sword-you-wanted +2 instead of the measly +1 you lost in the trap on the way there.
But sometimes, inexperienced GMs chose to do something to my character, that is so damaging in game terms that it is worse than death. Not necessarily in-character, but on a purely functional player level. I'd rather have that character killed, then continue to "play".
The example I remember best because it was so pointless was a Dark Sun campaign I played in school. We were wandering the desert and some beast attacked us. We fought, my character took a lot of damage. The GM decided that the monster had bitten of an arm and a leg of my character. Now, if you know D&D a little, that is way off book. Nothing like this exists in the rules, that is a pure GM decision. The campaign was level 2, it was supposed to maybe take us to level 4, so regenerating anything in the middle of the desert on level 2 was totally out of the question. For a wizard or priest that might have been a tough roleplaying challenge, but for a martial artist that this character had been, that was worse than death. Basically anything on the character sheet had become useless. The only thing the character could do was roll unmodified int or cha checks once in a while. I spent an hour disagreeing with anything anybody said just because I was angry and in the end just left and told them to call me if they decided I was allowed to play again.
How does this little story connect to your conflict? Well, in any system I have played so far, "the ship", whether that is an actual sailboat, spaceship or just the teams supertuned car or Truck they operate from, is owned by a player's character.
It was created as part of their character class. It was probably so expensive and so much of their character's resources at creation went into it, that just buying a new one or even repairing extensive damage is out of the question in a normal adventure. In Star Wars, one character might get a ship, another might be a force user. In Shadowrun, one character might get a car worth a fortune and another might be able to use magic.
The point is, this vehicle is part of the character. Damaging it is damaging the character and while regular, by the rules damage is just part of the adventure, if the DM just decides it got damaged by the story, you have to be very careful. If you damage it enough for the character to become way worse than they were when they started, the player will be frustrated. You would expect the Jedi's player to become frustrated when you decide a random dog bit them and they lost the force, or the Wizard's spellbook just disintegrated after a dog accidentially peed on it. You would not do that. It would damage their character beyong the point of repair for seemingly no good reason. And a ship is part of a specific character in any game I have played so far.
So my advice is, do not damage a player's character beyond the point of reasonable repair. That ruins their game and as a result they will be inclined to just take the game down with them by ruining it for everybody.
In this specific case, to not have a character become collateral damage to the story playing out, the dogs could have told the pilot that they are very sorry and they would pay the repair bill once they reached the other humans camp. Alternatively, if damaging that ship was important to the story, the ship should have been property of some third party altogether or you could have sat down with the players in session 0 and told them you will damage or destroy the ship and to be prepared for that.
As a last example: I don't mind my ship being blown to pieces for story reasons. Then I am the pilot without a ship and if the GM plans to give me another ship later in the story, it needs some good roleplaying, but fine. I do however mind the fact that I spent 5 hours thumbing through countless books trying to configure this ship, only to have it blown to pieces three minutes into the first session, not by bad luck, but purposefully by the DM. Why did I just spent 5 hours for nothing? The DM could just have said so and I could have picked a random default ship from the list done something useful with the remaining 4:58 hours.
To summarize all those examples into one generic advice for a system-agnostic answer:
Be aware how much damage your story causes to characters and do not damage any of them beyond repair. Because if you do, the player is unhappy and will become uncooperative. Whatever solution you pick to get over that specific problem at hand will not solve the fact they they are unhappy with your game.