It presents the option, but ultimately it is the PC's choice (as it should be) what approach they take, the module IMO shouldn't "try hard" to encourage the players to do anything. And I disagree that the goblins were "good" guys. The goblins robbed travelers along the Old Road until it fell out of use, the goblins are also working directly for Belak the Outcast so, regardless of reasons, they are furthering his plan and thus are not "good".
Ultimately, it is the players' choice. If, in your game, Goblins and Kobolds are evil, twisted creatures who can be slain with impunity by PC's, then why should they expect it to be different this time? In fact, if we bludgeon them with "well, these ones are different", then why are they different? But if, in your game, goblins and kobolds are like any other group - some good, some bad - and the expectation is not that the PC's first solution to every issue should be "kill them, loot the bodies and burn their village", then that is the approach I would expect the PC's to take here.
IOW, I agree that it's not the scenario's job to set your group's play style expectations.
First let's get this straight... they aren't sent by or hired by the villagers, read the hook again. Secondly the possibility of diplomacy is presented in the adventure itself so their mission is not to slay the goblins but to find out how/if the goblins are stealing the trees and where the fruit comes from... to heal their friend or ally. you keep presenting slaying the goblins as THE mission when it's not.
Again, play style. The mere presence of goblins means "kill the goblins" is the mission to some groups and some players. Others will see diplomacy as the first approach. That the scenario allows for both approaches seems, to me, a strength that was lacking in many of its predecessor adventures for 1e/2e.
What story, it's an adventure location... what the story is... is up to the actions taken by the party exploring it. The fact that numerous play groups ended up leaving the dungeon with a kobold friend named Meepo shows that there was a possible "sometimes monsters aren't really monsters" theme that could be explored through play but it was not the theme of The Sunless Citadel. Are you still harping on the apple thing... again the mission was not to...nevermind. Last but not least, no you do not need to hold the players hands a bit because you shouldn't be forcing a story on the players.
Play style. If the group is happy with "monsters are monsters - kobolds and goblins are evil, and kept so, irredeemably and irrevocably, by Goblin and Kobold deities - they exist only to be killed" as a justification for humanoid monsters as XP farms, then that's a valid playstyle. "
Gob-lin-oids are just the same as you and I - all bi-peds're brothers 'til the day we die" can also be a wonderful world excuse me, another valid playstyle. Now, if the group is divided on valid playstyle, that's a concern, but the scenario allows for both possibilities and many in between. It's not up to the scenario to start with "In this very specific case, attacking the monsters may not be your best approach and you should consider diplomacy just this once".