I think that its a dangerous business to try and pin down theological theories on Eru, the Valar and anything the legendarium, really. People tend to forget that Tolkien was not a Bible scholar* and so it would be unfair to try and fit a lot of theological ideas into his legends.
Tolkien's Illuvatar may well have his roots in many legends as well as the Biblical accounts, as davem has pointed out he had a similar name to Odin from Norse. Tolkien's expertise were in language and legends and we can't expect him to have all the answers to all the most difficult questions of life the universe and everything. The fall of Numenor, then, may be derived from the Atlantis legend which does include an arrogant people plotting war against the gods and so some harsh punishment had to be dealt out.
To say that Tolkien's Eru is some how a picture of his beliefs of God is a dangerous thing to do because here we have Eru placed in a legend that had nothing to do with the Jewish God and so to pin ideas of 'God is a meanie' or 'The Numenorians had every right to do such and such' is not a good road. If we want to find out the motives behind Eru or the Numenorians it might be better to look into the Atlantis legend and see what it says about it. I don't think that Tolkien's personal beliefs came into it and I think he just wanted to tell a story here. It would be like looking at the killing of Balder by the trickery of Loki and then asking a Jew or Christian, "Why would your God allow that?"
At least, that's what I thought anyway...
*Okay, neither was C.S. Lewis who seemed to get his head around complex theologies, but that's not my point... so... ignore that fact.
