I agree with all of this in principle, but in reality you have to draw a line. There are many things that were illegal in the past that we now consider perfectly fine and there were punishments in the past that we would now consider draconian. I mean, where do you stop, are we going to apologise to the population of Australia for what we did to some of their forebears?
The fact is this is actually a recognition that Turing's work during WWII makes him exceptional, so they're making a special effort and, indeed, an exception for him by making this formal declaration. The bare fact is nobody (or at least very very few people) now consider anyone who was convicted of something similar to Turing as being a criminal. We all know it happened, we all know it's wrong and we know we've learned to behave better. If there are people who were persecuted are still alive, some public declaration of their mistreatment would be reasonable. But at the end of the day, the dead don't care.
There are many things we as a nation did in the past which we as a nation today would not do. But history is a very long time and the past is done and can't be changed. Does pardoning people long in the grave really mean anything?