Atheism and morality

[Inigo]

What is in dispute is what it would for altruism to have moral goodness. We don't just judge altruism to be altruism. We judge it to have moral goodness.

When you say "we" who are you addressing in this statement, and do the people who you are addressing always see altruism as moral goodness no matter who it is directed at?

I don't always judge altruism to be moral goodness, there are some people who I think don't deserve as much concern or charity but who do get it, and I think it's totally wrong.

I've already mentioned this. Of course altruism is not always right. Sometimes it is right, sometimes it is wrong, sometimes it is supererogatory, sometimes it is subererogatory, sometimes it is permissible.
THe point, though, is that this is beside the point. When altruism is or is not a virtue is a matter in normative ethics. What we are talking about here is what morality 'is', not what it tells us to do and be.

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Why does morality have to be external instructions?

If it was an internal instruction (an instruction you issue to yourself) you would lack inescapable reason to comply with it.