None of those hooks have the PC's primary mission as "murdering the goblins". The villagers want the PC's to investigate whether the goblins are stealing their trees or not (theft being a time-honored reason for hunting down bandits but not goblins for some reason???), and the seeds of those fruits do something monstrous...
EDIT: In fact there is a section in the module about being diplomatic with the two major groups of anatgonists, and while harder it is not impossible to establish diplomatic relations with the goblins.
I did not recall that the DM notes indicated that this was a "diplomatic" mission. It doesn't seem like the module tried to hard to encourage players to assume the goblins probable innocence though. Usually a story gives you some kind of hint that the apparent bad guys are more than they seem. But fair enough, the module at least figleafs the fact that the goblins are really the good guys, even if the adventurers can't find this out until they've killed all of them.
However, I have to take issue with your second point. Sending adventurers after bandits is indeed a time honored D&D trope going back to at least "the Village of Hommlet". But to justify that, first you have to establish that there are, indeed, bandits. Slaying evil witches is
also a time honored fantasy trope, but I wouldn't want to run a module where the players are sent to kill a bunch of women because somebody "suspected" them of being witches.
Yes, the seeds of the fruit do something monstrous. And I think
Sunless Citadel has a great climax, and a really good Big Bad. It's also got some clever traps and tricks. I really like the structure and layout of the module. The only thing I don't like is that the goblins and kobolds are basically blameless victims in the whole charade. If the set up of the story had them killing and murdering the surrounding countryside, then sending adventurers to "deal with them" would be a great story.
Even if the intent of the story was to say "sometimes monsters aren't really monsters" (which I don't believe was the case, I think the writer actually
thought selling apples for profit was actually somehow villainous), that's pretty deep for an introductory adventure, which are supposed to be a bit more straightforward than that. And if you are going to go that way, you need to hold the players' hands a bit.