Firstly, to answer SpM, I too don't like what Eru did. But I can reconcile this as the action of Eru, who is a very odd kind of god. He's not the kindly sort of God that modern worshippers know, but more the Old Testament type of God who would happily smite you down just for fun, for a bit of a cosmic joke. He's like the God of the Book of Job who toys with even his most faithful followers and is let's be frank, a wee bit cruel. But he can do this simply because he is omnipotent, and in fact its the kind of thing you'd expect of an omnipotent god - play around with even the most faithful, just to keep them 'in their place'.
That's just how Eru is - and it works if you consider the difficulties Tolkien himself had with reconciling his belief in God with the real horrors he saw on the Somme (such horrors as none of us has ever seen so we can't even get to the point he must have got to). I have to say, this Eru who Tolkien turned up isn't someone I particularly like, but he's interesting enough as a literary creation, and he certainly gives the writer incredible licence to do dodgy things to his characters as it can all be explained away as "Eru did it", and we all go "Ahhhhh, I see......"
The nature of omnipotent gods is that they can be as horrible as nasty as they like, but we can't question their motives because they are beyond our own concept of morality.
Now, getting on to those evil little kiddies who drowned. I seriously doubt that Tolkien really believed that children playing at being Orcs meant said kids were by nature 'evil' - you only have to read biographical works on Tolkien to see just how much of a family man and devoted father he was. Such a man simply would not kill off children and want us to believe this was 'justified' - has anyone ever thought that he put this there so that we would question Eru's actions? We are allowed to, you know! Remember there is no final word to say that this here literary creation, Eru is God, and nobody/no deity is going to smite anyone who questions this Eru's actions against mere children!
The other character who concerns me is indeed Miriel. Tolkien does NOT set her up as evil! Where does she condone the actions of Sauron? She is simply trapped in a marriage she does not want. The reason she did not speak out is laid out in the story - she simply could not. Putting a modern analogy to this - there were many ordinary Germans during WWII who did not speak out against Hitler - but this does NOT mean they condoned his actions or were 'evil'! I believe there is a letter mentioning Tolkien's own belief that ordinary Germans should in no way be held 'to blame'. They were simply trapped in a situation where they were inable to speak out for fear of their own lives. Tolkien is not in the habit of creating figures who are martyrs - and he does not make one out of Miriel. Rather he invites us to view the very human tragedy of Miriel (and many others too) caught up in events outside their control, and invites us to ask questions, not to draw lines and prepare nooses.
Finally, back to Atlantis. I am afraid that one letter in which Elendil is called 'Noachian' does not turn Tolkien's story into a Noachian story, no matter how much we want it to be one. The overwhelming evidence is that this is simply has little if anything to do with the Biblical flood, it is to do with Tolkien's Atlantis complex. That one Noachian figure proceeds from the story certainly does not mean that the story itself is Noachian - that I am afraid is simply speculation as Tolkien tells us the story is not Noachian, it is Atlantean.