I like your second post as a potential.
See, I figure the results of a compromise last until challenged by another conflict. So, if the mice are driven of, they don’t simply have a Twist, then return. They have a Twist or other complication of the compromise, then drive into the next Obstacle. If the snake (or other conflict than this example) has been the second Obstacle (and you are not planning a third or more Obstacle) then the mice are driven off and into a safe place to begin the Player Turn.
During the Player Turn, the first check might be initiate a Conflict such as Fight Animal. Or, other checks might occur and a later check initiates the conflict. The players should have a tentative idea of what order they want to handle things.
However, if no one uses a check to challenge being driven away, they don’t face the snake again by my choice. They’ve somehow accepted being driven off and the snake has no reason to harass further.
Personally, I would accept the group saying, 'a check will pathfind our way to a new location, a check forages for food, then a check initiates a fight animal conflict with the snake, ‘cause it followed us along the way.’ I mean to say, I’d allow them to narratively force the snake to follow them; I’d allow them that authority over the NPC, since they are using a check to gain that. YMMV, that’s just my perspective on narrative authority.
So, in Grain Peddler, I think that determining whether the travelling merchant is alive or eaten by way of the initial confrontation with a snake is a good choice. It offers you a chance to really shift the focus from a mystery to an interrogation. They might even find the grain peddler is a good mouse, but forced into spying. Or maybe the grain peddler is only carrying personal letters, but doesn’t realize a relative in Lockhaven sent the map enclosed in a personal letter. In fact, that means there is a conspirator in Lockhaven and an armed rebellion in Barkstone?! What direction will the patrol take if they realize the enemy lies in both directions–back in Lockhaven as well as ahead in Barkstone.
In the case of an eaten grain peddler, not only are they driven away from the cart (at least for a time) and answers to the mission, they are also left with an undisputed feeling the grain peddler was guilty of treasonous activity. They might never really know the truth–just their perception of the truth. Later, they might encounter the grain peddler’s family in need of answers and help. They might misidentify him as a villain and denounce his family lineage among mice.
Anyhow, there are loads of directions to go. I’d say that second post of yours is a creative way to balance the choice whether the grain peddler is alive or eaten. It places the actions and results of the patrol in the center focal point of events in the story. They can secure safety and true answers about the grain peddler.
If instead, you pre-determine the grain peddler is eaten (which is actually how I’ve always used this mission), there is a surety that the evidence looks like guilt on the peddler’s shoulders. In fact, once, the patrol decided they had stopped the map from falling into the wrong hands and felt that finished off any conspiracy right then and there. They used the Player Turn to head toward Grasslake instead of trying to follow-up on anything related to the Barkstone contact or other conspiracy theories. (I gave them Trouble in Grasslake for the next session).