her ideals are pure and heroic because they're the Word of God and we know she's in the right because she has divine authority.
And that is something that will always be hard to completely buy. For me, at least. There's always an element of "because I say so" that rubs me the wrong way, whether it's my inner rebel or atheist, I'm not sure. But whatever, a comic with crazy sea monster wins out for me, in this instance. =)
If she stops worshipping the Patrons, she stops operating with their authority, and therefore stops being Wonder Woman and becomes just another random hero.
Okay, I can sort of see that point. But she doesn't stop being influenced by the morals, ideals or virtues valued by her (former) Patrons or Amazon culture. They are a part of her past and therefore she cannot ever be cut off from them. If Bruce Wayne's parents came back from the dead, his trauma would not heal and disappear. I see this more as her losing her official status, changing her daily life and of course disrupting her family, but that doesn't mean they're not her family anymore, or that Athena or any other patron doesn't hold importance to her or that their wishes don't have any sway over her anymore, even if she isn't officially bound to obey them.
The Bruce Wayne buying a gun analogy, is actually kind of misleading and confusing on my part, because while it did allude to the point you make about it being thematically wrong for Batman, it also actually happened. (Bruce Wayne: Murderer/Fugitive arc.) He bought a gun as a kind of therapy. Like he was trying it out, to see what doing it would be like. Wonder Woman no longer worshipping the gods and no longer being an Amazon can only be temporary, surely.
I mean, the way Achilles is shown here, he is clearly sympathetic to the Amazons now, and I can see him and Hippolyta teaming up to confront Zeus on his asshattery and demanding that Diana be allowed to return.
So I don't see this as something that is permanently changing or affecting the theme and status quo of Wonder Woman.