Queen Elizabeth is a life-long traditional Anglican, who must be appalled by the crisis. However, her hands are completely tied by the current system. She can only rubber-stamp what is given to her by the Archbishop of Canterbury. She does have influence with him but it's a secret how much she can influence church affairs as Defender of the Faith.
Another problem of her problems is Prince Charles, 'new-age'-influenced heir to the title, and openly living in sin. On the other hand, the Queen doesn't want him to marry his mistress either because she could have already used her influence with Rowan Williams to push this forward.
Here's a prediction. The Anglican Communion will split apart in October. The western portion (except for Bishop Duncan's Network) will stay under the Church of England. The rest will go along with the African Primates. Rowan Williams will push to allow Prince Charles to marry Camilla and this splits the evangelicals from the liberals in the Church of England's House of Bishops. All of this makes the Queen very unhappy but she has to give in because her hands are tied. Implosion of the worldwide Anglican Communion as we know it but watch the rise of the worldwide Anglican bible-based conservative Network.
I guess the bottom line question in my mind is whether or not HM is willing to exercise Royal Authority which still exists on paper, but hasn't been used in several hundred years.