Honestly, it sounds fine and logical to me. Let's face it, the return of the gods and their departure in the first place in Dragonlance were only treated as good and bad things respectively because that's what the authors (devout Mormons) believed they should be seen as - let's be honest, who here thought that the Cataclysm was at all a measured, justified response? Who didn't think the gods got told off properly for expecting mortalkind to immediately cower afterwards, especially since we know they took all the clerics away beforehand and then didn't send them back to tend to the injured or preach about how the Kingpriest, beloved "champion of good", had been misleading them? Mortals are supposed to be the ones at fault? It looks to me more like the gods got sniffy over being told off to me!
Seriously, a lot about Dragonlance grinds my gears, but the presentation of the gods as somehow actually morally perfect and superior, despite acting like classic pagan style gods (read: hubristic, arrogant, and prone to bringing their troubles upon themselves), is one of the biggest flaws.
Come to think of it, it's been too long since I read the first Chronicles book, but I'm pretty sure there's a part where someone - Tanis, I believe - actually does express doubt about whether or not they should want the gods to come back, even if they are the only source of healing magic in the setting.
...
Except "I don't think god/s exist" is the very definition of an atheist. Actively scorning or denying the existence of gods is maltheism, which nobody seems to be able to use straight - the Athar are classic D&D maltheists, and really in any of the established D&D settings outside of Eberron, maltheism would replace "atheism" entirely, since the gods are demonstrably real. You can argue about whether or not they are real gods, or if they deserve worship, but arguing that they don't exist is like arguing that fire won't burn you or water won't drown you.
Just popping in to clarify this character point: for my gnome wild mage, "maltheism" is a more apt description of his beliefs. His background was as a Hermit, and his Discovery is that he figured out what caused the cataclysm: the gods slaughtering millions of innocent people to preserve "The Balance." This is what he fears will happen with the gods "come back": that inevitably, they will think something is out of whack again at some point, and fix it by murdering millions of innocent people once again. His sincere belief is that if mortal free will ends up upsetting "the balance", and this destroys the world, that this is a much better fate than a never-ending cycle of diefic hyper-violence, because it was
freely chosen by the mortals. The gods can keep their meddling paws out of it (hell, the Balance was created by the gods in the first place, so maybe they can take that, too). The last few hundred years have proven that people can get along just fine without them, and it seems like one of them (Takhisis) coming back was the trigger for all this, so they can just grab her and go away again. If free will is to have any meaning, mortals must be free to exercise it without the gods correcting them when they do free will wrong.
This is an entirely reasonable position according to the lore I'm familiar with, and also one that has a unique resonance in Dragonlance, since DL has the rather unique distant history of a deific Cataclysm (FR has holy wars, but nothing like The Balance; Eberron's tragedy was mortal-made, as was Dark Sun's, though no one remembers the latter).
That this character is somehow "illegitimate" to my fellow-players is a problem. I care about setting canon, because I want to create characters whose stories are unique to the settings they're in, characters tethered deeply and inextricably with their settings, whose motives and goals make sense using the setting's assumptions. That's fun for me! One of the things I like about of D&D as a hobby is the performance of a character, which means being clear about what characters work within the established world. So when someone else points to some different canon as some reason that my performance isn't authentic, that sucks the fun out of it. So, I'd like to minimize the possibility for that to happen - and every time you change a bit of lore, it increases the chance that this will happen. (It's effectively the cardinal sin of improv - it negates. It says "no.")
This doesn't mean I want Canon A or Canon B. I don't give two flying gerbils what Weiss and Hickman make in their world - that's up to them. But if I don't know what the expectations are, I can't be reasonably expected to meet them!
If gnomes couldn't be wild mages and every character had to want the gods to come back and the DL books basically just came out and said that, that'd be fine, too. But that's not what the sources I read said. I've no investment in any particular lore, I don't care what the lore is, but whatever it is, I want to
use it, and to share that experience with others at the table. Yeah, it'll never be absolutely perfect - there's house alterations, there's necessary updates, that's fine, I'm not advocating for some unchanging ideal. I do want to note the real
cost of that change, though, and to note that it's significant. So if you think you have a better idea for what tieflings or gnolls are, you better understand what they are already
exceptionally well, and you better be prepared to cause some perhaps-minor / perhaps-significant conflicts at some tables because of your change. You are creating a more significant barrier to understanding your weird game about imaginary elves, and a more significant barrier to appreciating and using world-lore in play. That doesn't mean don't do it. It means know what you're getting into when you do it.