From your link:
Quote:
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The pardon was granted under the Royal Prerogative of Mercy after a request by Justice Minister Chris Grayling.
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In other words it was the government that moved on it, not the Queen. Most of the royal prerogatives are actually exercised by government ministers these days - or by the queen, "on advice".
Also, having gay friends or speaking in general terms in favour of equality isn't the same as lobbying the government on a specific item of business. William has acted perfectly correctly.