Actually, the Secretary of State for Justice has the power to grant a royal pardon, and notably exercised it just the other day:
http://en.wikipedia.org/wiki/Conviction_of_Michael_Shields#R...
http://en.wikipedia.org/wiki/Conviction_of_Michael_Shields#R...
"... I have recommended to Her Majesty the Queen that he should be granted a free pardon and she has graciously assented."