I would suggest creating sufficient doubts and flaws on its part to allow readers to think that this entity could surely not be god, yet at the same time remain close enough to the source material to suggest that it might be anyway. Just not the "real real one", if you know what I mean.
It will be clear to the reader that the entity really is the same entity described in the OT. It will not be clear to the reader what this entity really is in the universal sense.
The real question of course, is what makes those Sat-an character(s) so different from everyone else that this 'god' does not just kill them outright while claiming them to be unbelievers. There has to some kind of motivation to why this god cannot just do these things. After all, while religions may thrive on religious criticism (according to some), there are very fine lines to thread while making such criticism heard.
And what happens when "angels" are destroyed by the unbelievers? (in a materialist fiction, and certainly one where god is not perfect and a character, this is a likely result)
The story implies that the last time God was around, something happened that caused him to to end up working on borrowed time. It's clear to the reader that God cannot
or does not want to intervene too much (the extent remains blurry to the reader, gives me lots of margin). The fact he was working with limited time is why he left, but has now finally returned, as he knew he would one day, and this is important to explain why he needed "a people" among all of the people of the Earth.
Might as well explain what actually happens to some extent: God was overseeing two humans (Adam and Eve), but shit happened and the creatures multiplied. God put his watchers in charge, because there was too many people to deal with. The goal was to make sure all humans would continue to worship him, so that when he would return thousands of years later, he would not be in a position of confrontation with what would likely be a much more advanced race than they were at the time. That is the point of "worship"; to be welcomed as God on his return, with open arms, rather than be welcomed as a space-invader-thing, with a nuke to the face.
But it didn't work, humans worshipped the Watchers, saw them as gods, etc., tried to outdo each others in feats (Sumerians/Babylonians/Tower of Babel, etc.). God was angry with the work of the Watchers and the impact on mankind's development, caused the flood to try and start things over with limited numbers of humans again. Old problems arose again over time, and God said "fuck it, I can't control all of mankind, it doesn't work, it only leads to problems and too much micro-management, there's no way they'll still be worshipping me on my return, their in-fighting will lead to enlightenment and rapid advancement and the rejection of God(s)". So he chose to make himself "a people among the people" who would worship him until his return, he would just really put more effort to make sure they would be likely to still be worshipping him even if he had to leave for a long time, and since they would be exclusive they would naturally be more likely to "try to survive/maintain their beliefs", especially if he provides them with an ever-lasting "promised land". That way he could ignore the rest of mankind, and simply keep these ones as his people, regardless of how the others would behave. It would be up to them to try and survive and keep their faith, but it was the best plan according to his goal. So upon his return, while most of Earth might see him in a confrontational manner, there would still be a people waiting for him. He'd just have to get rid of the others, or ask them to fall in line. To him this is the better alternative, rather than risk war with all of mankind on his return and having to start ALL over again.
That's the writer's perspective I'm explaining, my intention is not to make this obvious to the reader, as to me it's vital that the reader wonders if the protagonist is really doing the right thing. A lot of details (God's plan, etc., are not mentioned here).
The main question of the book, in a way, is "An existence of immortality in submission, or a mortal life with freedom?". The hero chooses the later, but he and the viewer must wonder if ultimately it really was the best decision. The hero ends up leaving into the "void of space", which is the reminiscent of the rejection of God, or the equivalent of choosing hell. But is it really hell, or actually heaven, figuratively speaking? Hell = void, away from god, emptiness. But space also represents the sky, the stars, hence heaven?
That's the gist of the story. There are more parallels of the sort but that's the idea. And the overall decision the protagonist has to take, in a way, is a true exercise of faith, since the consequences of his choice are unknowable.
Write what you consider to be true, or alike to the truth. So far your justifications, one way or another do not, to me, demonstrate, a good grasp of the material you are claiming to write from.
What do I know really? But you don't want to be a historian who can only name a handful of emperors. Research is key. If you are writing from the Jewish viewpoint, but criticizing the Jewish god like an outsider, it may ruin the authenticity of the storytelling.
No worries, I'm really summing up things quickly here. There is a margin of error in terms of what the OT says and what really happened, since in my book the OT was still just written by humans, and is not an actual recording of past events, just a written account from the perspective of those who wrote it, but a relatively good indication of what happened from a human perspective.