I don't know, Sqad I think the 'badness' of the law should be taken into account. If Turing had, say, been a convicted pedophile, then he quite rightly wouldn't have been pardoned.
And you're right - they can't pardon every single man who was prosecuted under the old law. But Turing is something of an iconic figure in the gay community, and pardoning him sends a message that effectively applies to more anonymous cases which the state does not have time to issue pardons for.