I don't presume to tell my Queen what she should and should not do, but if she did feel that way, she should - and would have - done so according to the principle of British Constitutional Monarchy. Which is that - in private - she has the right to warn the Prime Minister that she believes this is wrong.
She does not and can not speak out against Her Majesty's Government in public. She can and does do so in private. And because it's in private, unless she or the Prime Minister leaks it - and the Queen never has, and Prime Ministers virtually never have - nobody would know.
She has the right to be informed, to be consulted, to encourage, and to warn - in private. That is the way it works.
Oh, pardon me, but what would happen if she did? Would it be worse than inflicting gay marriage on a people who were once, and in some quarters still considered, the leader of Western civilization and defender of Christendom? What would they do, insist she step down if she made a speech on television upholding the religious and social value of blood family, which is after all the source of her office and that of her children? UK already had civil marriage, so what good can possibly come of the government forcing the church to eat crap? Are you saying the Parliament would interrupt her Jubilee and make her surrender her crown?