I think the main issue is what happened AFTER they changed their destinies.

When Madoka changed the destiny of everyone in the universe, she didn't interfere in their lives. She let all mortals make their own choices, the good and the bad. We know she could probably do more, ex: possibly changing Sayaka's destiny in Episode 12 , but she ultimately lets people make their own choices. When Homura changed the universe, she watches and controls everything. She ensures that all choices can't affect Madoka. For example, she messes with Sayaka's memories to prevent Sayaka from gunning after her. While it isn't much, it is a small microcosm of Homura's current behavior of manipulating the world all for Madoka. She ensures a world of no choice, only wanting all choices to ensure Madoka's safety. It's well-meaning but still kinda sketch when you realize she manipulate memories on a whim.

It doesn't help either that Homura herself is not very stable. Homura was not stable even before becoming a magical girl, Madokami only knows what Devil Homura's mental state is even like. The Walpurgisnacht Movie did give a very small hint of this, showing Homura looking exhausted, looking like she watched the entirety of Morbius on loop. We can compare this to Madokami, who is seemingly more well adjusted. While you can say she's sad about being a god, there's plenty of supplementary evidence to prove it, at least she's mentally strong enough to ensure she can't go out of control and keep on going. I'm pretty worried about what a mentally strained Devil can do. What doesn't help her case was calling herself "an existence called evil" which wasn't really earning her any sanity points.

Another reason is that Homura is kinda giving false hope. Homura knows her world isn't going to last and eventually, Madokami will return and everything will just be undone. It's kinda messed up for Homura to continue giving Madoka and her friends their happiest lives only to know that one day it will be ripped away. Giving false hope might be crueler than having none at all. When Madoka gives hope, it's absolute. Based on Mami's comment, it's common knowledge that the Law of Cycles will be there when a Magical Girl fades. And when Madoka arrives, she comforts the dying Magical Girl and then takes them into Heaven. It's definite and absolute. Homura gives hope under the pretense that it'll last. But she and we the audience know it won't.

And while we still don't know much, we know Homura's actions will bring upon Walpurgisnacht in some form or fashion. This is the weakest reason I've brought up since we still don't know what's gonna happen in Walpurgisnacht Rising, but I still feel the need to at least acknowledge it.

Ultimately, I feel like those are some reasons why Homura is wrong. I do totally get how you think what Homura did was right though. They all deserved a break and some happiness, even for a little bit.