I agree that realistically there was no way the Queen could have refused permission for the marriage, even if theoretically she had that right.
However, I think for Meghan to become a senior working royal immediately was a very bad idea, and not only in retrospect. Putting aside what we think of her as a person, she was an American citizen who had barely any experience of life in Britain, let alone life as a royal. She could have still married Harry but taken time to ease into royal life, maybe doing occasional engagements while getting to know what her role entailed. There was no need for her to be a full time royal straight after marriage, especially as it was likely she'd be wanting to start a family soon.
I wonder if it would have helped if Britain had the same convention as other royal familes, whereby 'married ins' are granted citizenship of the new country upon marriage, and are often required to renounce any other nationalities they might have. Queen Mary of Denmark had to give up her Australian and British passports upon marriage, for example. Of course, she was married to the Crown Prince so you could say it's different from Meghan, but the wives of the Danish 'spare' also had to acquire Danish citizenship and renounce their own. The husband of Princess Madeleine of Sweden is also not considered 'royal' because he declined the offer of Swedish nationality and retained his British and American passports.
Maybe it would have encouraged Meghan to take her future role more seriously if something similar had been asked of her? Then again, given how sensitive immigration matters are, it would have caused a lot of controversy if a member of the royal family could 'skip the queue' for citizenship. I do think the royals were in a 'no win' situation, and I agree with the person above who said they bent over backwards trying to accommodate Meghan, but nothing was ever enough for her and her husband. I remember the person quoted in the Valentine Low book who said something along the lines of 'The mistake we made was thinking they wanted to be happy, when in reality, they had a whole other agenda'.
It was never going to work.