I think a lot of the issue comes down to the way goblins are portrayed in this game in particular.
Historically in fantasy computer games, Goblins were often portrayed as largely mindless monsters. Cannon fodder. Mooks to be mowed down. Sometimes you got a bit more flavor than that, a tiny bit of (generally) hostile dialogue, but even then goblins were usually portrayed as warbands of able-bodied soldiers. You didn't really get to see non-combatants.
BG3 is different because the Goblins are fully rendered, usually have names, and dialogue options. They are not portrayed as monsters, they are portrayed as people. This makes it a bit squeamish to consider as a "good" character just slaughtering the lot of them.