You know the broad strokes from here on out. Where things take a notable departure is in Noah's attitude, and immediate circumstances. The Bible is pretty clear that Noah's sons all had wives, and that God and Noah were on the same page about being fruitful and multiplying from day one. Here, only Shem is of marrying age, and betrothed to Noah's adopted daughter at that. Japheth is too young to think of such things even by Old Testament-era standards, and Ham is pissy that he has no woman. All of which intensifies when Noah has a vision of himself as a demon, and determines that even he and his family are so fallen that the human race must end with them, and therefore any potential grandchildren must die. It is entirely likely that a man in such circumstances could think in such a manner, especially after consenting to assist in what is basically genocide; yet to those who believe, I can see how it is tantamount to slander of a beloved prophet.
To me, however, and to Aronofsky, it is more than just the sum of its obvious parts in a universe of parameters; to see it as only the surface story is to deny it the power it has held as more than that for millennia. In the larger scheme of things, this take on Noah is one of post-traumatic stress disorder, and the burdens of doing right even when it means piling sins upon yourself. Like any soldier who must kill for the greater good, or any patriarch making sacrifices for the betterment of the family, violating conscience and eating away at soul for what must be done, Russell Crowe's Noah loses some of himself while sacrificing for the greater plan. Whether it be with family or God in mind, the things he feels he must do in service of all creation require the ultimate act of being a man, while enduring a burden none should bear. The extent you relate to that will likely determine how strongly you react to Noah...and Aronofsky, whose movies nearly always feature a semi-delusional protagonist sacrificing all for a larger cause, clearly feels that from the Genesis tale.
Crowe isn't a bad choice for the guy who can be a strong family man when he needs to, and scary psycho the next, but it is a shame that the one actor who would be even more perfect is currently, effectively blacklisted. I speak, of course, of Mel Gibson, who would likely have had less trouble getting the Pope to watch his film, and undoubtedly, sincerely believes everything herein. Winstone is fine as villain Tubal-Cain, but his character is a fundamental mistake. There isn't any need, for instance, to have him survive the flood if you're already going to play up interfamilial tensions - the narrative choice here is to have Ham ultimately choose his own exile rather to dramatically leave as a result of a nudity curse, and Logan Lerman's Ham is not only perfectly capable of playing that, but he's also given enough narrative material to justify it without the presence of an evil father figure to seduce him.
It has always struck me as ironic that most "faith-based" movies I've seen in my time, be they Christian, Mormon or Muslim, tend toward the saccharine and the sanitized, when all those faiths' actual origin tales are anything but (seriously, scripture is brutal). To the extent that artistic dissent is allowed, it seems to only be done so when based on a creative talent who explicitly professed faith, hence why JRR Tolkien and CS Lewis get the fantasy pass that JK Rowling does not, and why Mel Gibson can get an R rating and still be okayed. Aronofsky is not especially religious, but he understands the power of foundational myths. It may be asking a lot of some, but if you can avoid clinging to the literal in his movie and see the deeper emotional truths beneath, it just may move you to feel the pain of doing right, and embracing it anyway, not always knowing how far is too far.