I agree the Valar weren't angry with the Numenoreans any more than they were angry with the Noldor, just hurt and bewildered and unable to understand why the Children were acting this way.
The standard story is that Tar-Miriel was 'forced' to marry her cousin and share her throne with him. But in HoME we find an alternate tradition. According to this account Miriel had always loved her cousin and gladly accepted him as her husband and co-ruler. It's even possible that their marriage was seen as a good thing, for all it's unconventionality, a way of mending the rift between King's Men and Faithful.
We must also remember that Ar-Pharazon was not always evil. Had in fact been a close friend of Amandil and Elendil at one time. The real Darkening of Numenor doesn't begin until Sauron enters the picture.
There's no question but the Numenorean's rebellious and resentful feelings towards the Valar made them easy prey for Sauron, just as the Noldor's sense of being smothered made them more inclined to listen to Melkor.
The Valar seem to have panicked a bit when Ar-Pharazon attacked. Anyway they turned the whole mess over to Eru who fixed things by changing the shape of the world and so removing Aman from Men's reach - for our own good as much as that of the Valar.
The destruction of Numenor was less a deliberate punishment than an inevitable result of this drastic action. Even Eru is bound to some extent by the natural laws he has laid down. The Downfall thus resulted directly from the Numenorean's own actions rather than being an arbitrary act on Eru's part.
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