Pragmatic Morality

I have had a few discussions recently with friends, and on the usual forums, about morality. More specifically about whether or not a god is the source of all morality. I have no intention to rehash that debate here, because I have come to the conclusion that we have been asking the wrong question and looking at it all wrong.
The question about whether or not morality comes from god is an interesting one, but one about which there is simply not any evidence to support much on either side. In any case I don't think it really matters.
I am willing to grant, for the sake of argument, that god is the actual source of all morality. But my next question then becomes a problem for believers. What exactly does god have to say about morality?
If you are believer you probably view your particular set of morals as the ones god has commanded, but how is an outside observer to tell the difference?
Consider a thought experiment. Let's say that first contact occurs and that an alien but very human-like species lands somewhere on earth. Think Star Trek aliens, but hopefully more vulcan than klingon. They have no prior knowledge if human culture, thought, or religion. How would they know which version of morality to follow? To what books or people would you refer them?
Would you have them read the Bible? I have no intention of getting into detail about this but if you think the bible is a good source of morality you should read it.
The Koran? I assume most Muslims would say so, but if that is true I urge them to read their own holy book as well.
The Book of Mormon? A better attempt but still has plenty of problems.
I could go on and on but I think we can easily see that any religious book someone proposes is going to present problems, mostly for the people who don't belong to that religion.
What about religious leaders?
Most of these sources would say similar things about the vast majority of moral questions. The question of whether you should murder your children has a nearly unanimously agreed upon answer. These aliens could get the answers to the majority of moral questions from my kindergartener.
It is in the fine details where they differ. But within those fine details they have such a wide variety of views that it is impossible for any impartial observer to say which one of them is really speaking for god.
Which brings me to pragmatic morality. Since we cannot ever realistically use god to answer our questions about morality we are just going to have to do the best we can on our own. If there is a god I assume he would know the situation and understand.
So how do we pragmatically answer these questions? I think we use the most valuable tool that we have as humans, our intelligence. We use, reason, logic, and evidence to determine what moral behavior is healthy for humans and what behavior isn't. While at the same time being tolerant of honest differences of opinion. There doesn't have to be just one answer about how to live a moral life.