What you are talking about here reminds me of the first Witcher game (it is something that was in the subsequent games but much more subtle there) the idea of a choice coming back to bite you in the ass much later down the line or creating unexpected results. But if that is what Larian tried to do here, they still failed. Even in the smallest choices of that nature in the Witcher, you had something to gain and something to lose from each choice and you had some vague idea of what that is. There might be other consequences you were not aware of, but there were risks and rewards that were instantly appearnt.
In our case it is simply not so. Even a cheotic evil character can kill as many goblins as tieflings, so unless you roleplay as a tiefling racisi or a goblin lover chaotic evil character, there is absolutely no reason to choose to kill all the tieflings and not all the goblins. Killing all the goblins will lead you to a solid lead to solving your problem, and killing all the tieflings is... What Mintara told you to do so it's evil?
Yes, I think it could be much like TW1 quests (although I see a lot of links with deities/factions so I think it could directly affect their power). So sad there weren't a lot of quests like Whispering Hillock Spirit in TW3. And I agree, it's frustrating not to know right now. As I said, I hope it's obvious once we leave Moonrise.
I think evil character should just get enough information from both to know they are useless (Halsin doesn't even tell you anything before you kill the leaders, so he is also manipulating you and than just wants to get to Moonrise...) do some other encounters and/or exploration to get XP and head to Moonrise. I know it's doable to be level 4 without engaging with either of them. I know I will be speedrunning there once the game releases... I need to know.
“There is only one thing we say to Death: Not today.”