While I'm aware of some media that does not only portray Yahweh in a negative light (as he rightfully should be) but also casts him as outright evil and a force to be opposed and destroyed, none of this is in the mainstream or if they try to they just shove some expy of him instead of just outright stating “this is the Abrahamic God, he's the villain of the story.” In Japan, they got no issue with this in the game series Shin Megami Tensei where he goes by YHVH and in pretty much all of them he's an asshole with some of them having him as the true final boss.

As an aside, in the last entry in the series (Shin Megami Tensei IV Apocalypse) after killing him he slips from the minds of humanity (but could be brought back if enough people still believed and longed for his kind of law and order (pretty much embodies the “As Long As There is Evil” trope). So you could either (depending on how you got to him) just let humanity be afterwards and let humans and demons find their own path OR, you could usurp him, taking his place as the Supreme Being of the universe and remake it in your own image (while killing every last life form in existence other than your servants). The former meaning that YHVH can one day COME BACK while the later prevents him from coming back because you remade humans in your own image so there's no one left to believe in him).

Now, as we all know, in English speaking countries, we're far off from having a mainstream, high budget English speaking region made game/movie/television series where Yahweh is portrayed as a villain and looking to kill the so-called “Almighty” is considered a good thing (and even less likely that the humans would be allowed to WIN against him) with an all-star cast. At this rate there doesn't seem to be anything coming down the pipe where a heroic or Anti-Heroic Atheist (or a group of them) kills this so-called “One True God” and take all the religions with him, discrediting them forever and possibly heralding in a Second Age of Enlightenment, or the Age of Reason in the main stream conscious.

So with that in mind, how would you go about making a movie/game/television series where the God of Abraham was the bad guy with an Atheist Main Character who's goal was to kill him and it being treated as a good thing? I wouldn't be too sure how to go about it yet, but one thing I would be sure to do is to make sure Yahweh isn't pathetic (and I know the temptation to make him look pathetic is all too tempting), because if he turns out to be someone lame looking and overall impotent, it doesn't make for a compelling story nor for a believable threat. He'd have to be a serious, epic threat that could end everything. I'd play up the arrogance to make him hammy and a show off too. Also, Satan (and demons in general) would be a good guy and ally to humanity.