But, again, that's the point. It's not asking you to consider these things as good. It's telling you that in the context of this setting, this is what good is. It's very much old Testament, old school religion where smite the unbeliever was considered a good thing.
I'd actually argue that if you aren't willing to wrap your head around that mindset going into the setting, then this setting likely isn't for you. It's not trying to tell you to change your mind. It's presenting a very specific version of morality from a very specific viewpoint. Which, frankly, at the time it was being written, wasn't really all that out of line with a lot of mainstream thinking about things.
This is a setting where the ends 100% justify the means. That's the point. Remember, it's all about balance. So extreme good is just as horrific as extreme evil. It's unfortunate that they tied it to good/evil instead of law/chaos, because then it would have worked SOOOO much better. Everyone can get behind the notion of extreme Law or extreme chaos being horrific and bad. And, when Dragonlance was being written, Law/Chaos was largely the dichotomy in the game. Remember, Takhisis is the Queen of CHAOS, not the Queen of Evil. I think if you stop applying Good/Evil and see the conflict through Law/Chaos, it makes a lot more sense. The Kingpriest caused the Cataclysm, not because he was evil (that can be argued) but because he was too Lawful. The gods needed to shift things away from rigid cultures that stultify and die, so, whack, here comes a honking big mountain.
Takhisis is resisted because she brings too much chaos - if she wins, then there is no more order in the world - only the strong rule. It's anarchy. Everything has to be balanced. Not between good and evil, because that's too nebulous. But between Law and Chaos.
I really do think that a lot of the whole Good vs Evil thing is more what people are reading into the material, not what's actually there.