Well, you present an interesting situation, and I need to clarify something about it.
You described that the patrol split into two teams: (1) evacuate Grasslake and (2) drive off with fire. Just looking at those two items, you’ve got a complex Fight Animal conflict already. In fact, I’m certain that in itself was a great conflict to play through.
Now, at what point did the player want to perform the special kill move? During the conflict? As a member of one of the teams? Was the player acting alone?
So, my first advice is to restrict the situation when a conflict arises in the following manner: GM has a side and Players have a side. Typically, the GM has one or more NPCs while players have one or more PCs. Generally, the GM does not have multiple teams, but players might rarely have multiple teams. Everyone among the players joins a side and a team! No loners on a third side! In fact, no third side–GM side/Player side.
When sides and teams are arranged, then discuss goals for the conflict. This is another point about the player’s declaration which is a bit confusing. Was that special kill move the entire goal, or a described Attack? If it was the entire goal, that’s a bit too specific and doesn’t respect the rules about Natural Order. I’d pause to remind said player of the rules by identifying that this beast is too far above the order of mice to be threatened by mouse weapons in such a maneuver. I’d further clarify that the patrol could work together toward killing the beast (even including the special kill move) by a follow-up conflict (possibly), but to gain the follow-up conflict, they would need to rouse the town to action in one of three ways: (1) trained and hardened soldiers, (2) cunning and tough hunters, (3) poison by science. This would mean the problem is presented, and the players would all have to agree their side was about one of those three options and willing to work hard to gain the follow-up conflict leading to a kill. In the opening conflict, they would have to set a goal that distinctly identifies the goal of causing serious Injured or Sick condition on the snapping turtle with little to no loss.
In that way, they’ve gathered a force or caused toxic shock, and are more capable of threatening the snapping turtle. It gives a chance to now engage in a Fight Animal conflict where I’d consider the snapping turtle at a lower natural order.
It is a touchy subject, and each play group might handle it differently.
I suggest making the clarity about what can or cannot be threatened with death before rolling Dispo to ensure everyone is on the same page.
If the GM allows for the kill statement to be placed in the conflict Goal, and the team wins, you can still look at the degree of compromise. I mean this regardless of whether the GM placed a kill statement in the conflict goal. I often have different stakes than the players, so just having the patrol trying to kill a beast doesn’t mean the beast is trying to kill the patrol.
Using the degree of compromise, as well as guidelines in the rules text from page 130-131, the players must place the highest effort on complete success without losing Dispo in order to really gain the kill condition. From there, also consider the guidelines in the rules text from page 115-116. That holds a lot of clues about how to really twist the circumstances of success and failure during a conflict.
The last thought I’d really consider is how much the other players agreed or played along. Were other players suggesting this would work? Were the PCs warning each other not to get in the range of that snapping jaw? Although you have loads of info as the GM, the players might not fully understand the point-of-view which the mice have of such a beastly creature. So, maybe they were forgetful of their place in the world, let it be, and develop more clear descriptions for the future to tell the players how mice feel, think, and react when faced with such outrageous bravery, terror, danger, etc.
It isn’t D&D.