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We can choose to develop a moral system that goes against the principles of natural selection,

You're mixing things up here. Nothing can go "against" natural selection. If you go against it, you die, and you aren't selected anymore.

The process is still going on. There are obsolete and extinct religions. They promoted behaviours that were selected against and eventually died off.

It is the 'concept' of morality that is important here. The idea that there are 'right' and 'wrong' behaviours. Where did that idea come from? Came from not jumping off the cliff just because the deer did. Came from not picking up the rattlesnake or trying to handle fire. Just because a given action doesn't at first appear to further the survival of the species doesn't mean it doesn't in the long run. This concept comes from the requirements of survival. Like lemmings. That individual behaviour is destructive of the individual but preserves the specie.

What you call 'morality' by which you mean 'altruistic behaviour' in our former tribal conditions had the goal of preserving the genetic inheritance of the tribe, since it was likely that one was related genetically to everyone else in the tribe. And in preserving the tribe one preserved the protection the tribe afforded. That this was more successful a survival tactic than going it 'alone', so to speak, means that it was selected for.

if we assume that moral principles can and often do contradict evolutionary principles

Thus this assumption though is unwarranted.

You're mixing things up here. Nothing can go "against" natural selection. If you go against it, you die, and you aren't selected anymore.

First, we're discussing things at a number of different levels of analysis. Let's clarify first.

1. Individual vs species
Principles of natural selection do not really apply to individuals. They are principles that describe the 'evolution' of species. Individuals can and often do go against principles of natural selection. That is, they often engage in behaviors that, if performed by the species as a whole, would probably lead to extinction of the species. But the same behavior may or may not lead to the death of the individual.

For example, many couples decide not to have children, as a personal preference. This behavior defies the principle of natural selection, which would predict that all couples would want children in order to pass off their genes to another generation. This couple doesn't want to do that. They don't care. Their behavior cannot be explained by principles of natural selection. It doesn't make sense within that framework. AND their behavior does not lead to the extinction of the species, because a lot of other humans are having children. The species lives on. The only way this behavior would impact the species is if this behavior was a general trend in the entire population of humans.

So, people can have personal preferences or beliefs about what is "right" or "good" conduct that defy the principle of natural selection.

But you're right: we're not particularly interested in personal preference. When we discuss moral principles, we are concerned with universal principles of right or good conduct. We are concerned with concepts that transcend individual lives.

2. Is morality dependent or independent of natural selection?

This is the meat and potatoes question. When we are discussing principles of right or good conduct (morality), is it meaningful to explain or justify right or good conduct based on principles of natural selection? I say no, it isn't meaningful. Why? Because principles of natural selection are indifferent to moral concerns. They just are what they they are. That a behavior increases or decreases the chances of a species' survival says nothing about the moral justification for that behavior.

But more importantly, issues of morality are largely independent or unrelated to principles of natural selection. Only a relatively narrow range of behaviors involve issues of survival (life or death issues). What about everything else? Can't a behavior be moral without having conseqences for survival of the species? Surely.

In this sense, morality can be interpreted independent of principles of natural selection. Moral issues are concerned with good behavior, and good behavior can be defined in a variety of ways, but it need not be defined in terms of natural selection, unless issues of the survival of the species are a central concern. In these cases where survival of the species is a central concern, I would concede that natural selection is relevant, but otherwise, no, it is not. Morality must otherwise be founded on a more intrinsic set of principles of right conduct.