Morality changes with time. The laws have been changed to reflect. The UK government is saying that they can't pardon something that at the time was a crime and was prosecuted properly. I don't see that as immoral even if I find the past law immoral.

The are many things considered morally wrong by enough people to make them illegal. Assisted Suicide is an example. If it ever becomes legal, should everyone who was arrested and convicted under the current laws be pardoned? many people today would find that immoral.

Edit: Some in other threads have a raised another good point, what about things that are now considered crimes? Should we retroactively prosecute these people?