A lot of the trouble with Dragonlance's morality comes down to the alignment system, obviously. The alignment system is notoriously bad at actually representing anything as complicated as morality remotely well. Alignment in D&D started out as Moorcock's law vs chaos and did a weird thing where it took basically the same concepts and labeled them good and evil...but also kept the words law and chaos just to make things complicated. But law =/= good and chaos =/= evil.
If we replace "good" with the original "law," then swap out "evil" for the original "chaos" things clear up rather nicely.
The Kingpriest was concerned about law, people following the law, and with upholding the law. He didn't care about morality (clearly) he cared about order. People following the rules. He was an authoritarian. His motivations might have been good, maybe...initially, but his fanaticism for order at any price twisted him from good to evil.
This also helps the idea of maintaining balance actually make sense. Too much order is bad, just like too much chaos is bad.
And all this because people can't see the potential for evil in order or the potential for good in chaos.
Yes, I'm aware this isn't how it's presented officially. So what? The novel version is simplistic and kinda dumb.