Considering that there was an investigation following rumours of Columbus' misdeeds, and the fact he was imprisoned at all, suggests that moral standards haven't changed much. I think in general what is acceptable and what isn't (in the mind of the majority, should perhaps be added) hasn't changed dramatically throughout history as it is fundamentally based on social interaction and empathy, or so I believe. What I think might change is our view of other people and whether they are considered as equal and thus entitled to the same rights as oneself. That view can vary depending on culture, ideology or religion. Does that make any sense?
Personally I think moral standards alter over time. But they don't evolve into something completely different. For lots of reasons, some things that were considered awful then will still be considered awful today, while others, will not. Exactly because it is based on both society and empathy like you said, there are things the old societies deemed moral which modern societies would absolutely not. Despite the natural empathy in humans, it goes to show that morality was, not wildly, but still different in significant aspects, the further back you go, over the ages. It's like they have 2 components, one is based on basic human feelings and instincts, (empathy), the other is based on the world around the people. The latter changes, while the former does not.
Our view of people changes through various ways, and it shares a connection with the world around us. As the view of the general population towards people changes, so does the society and by extend, the moral standards. While it also works the other way around. As the society changes, so do the views on humanity and morality.
On a more personal level, this view is formed depending on the culture and society one is raised in, but to change, I think it needs radical new experiences in the individual's lifetime. Travelling to far away lands, coming in contact with new cultures, new religions and keeping an open mind while doing so (Spanish conquistadors' worldview probably did not change much when they came across the civilisations of South America ).
The other way one can get radical new experiences of course is shock. Coming into contact with something that you did not even imagine has a way of altering your view of the world. Something shocking that became widespread news could alter that vision for a lot of people, contributing on its own to the alteration of morality standards in a society.
Since widespread news wasn't available in the 15th century, maybe that's why the people in charge were okay pardoning him.
I do not know about the general populace's reaction, though historical experience shows that the reaction of the people reached its peak when said people suffered hardships and unfairness (like the French Revolution, or the worker strikes).
Which in turn makes sense, because the lower classes already led a very poor, dangerous and unfair life, trying to survive.
As such, I think that the people in charge of pardoning Columbus did not really consider the reaction of the people as any serious threat. And of course there was also no easy way to make it widespread news in the 15th century like you said.
