Optimizing for the whole is different than optimizing for the parts.
What seems redundant on a high level can be critical on a lower level.
To each antilope eating grass is purposeful. As may be the work of each Department in your original example.
Christianity arguably disagrees with you - see the tale of Onan. Buddhists likewise consider all life as sacred, in that an animal may previously/subsequently be a human soul. Lastly, many atheist progressives would argue that preservation of the human race is a moral imperative, and having more total humans rather than less ensures preservation in at least a simplistic mathematical sense.
"Be fruitful and multiply" is Genesis 1:28.
Onan is, per Jermone and canonical discussions, about spilling seed unnecessarily, but is more about not raping your sister-in-law and betraying dead family than it is about having many children. Nothing in there about the sacredness of babies or anything.
Onan's brother died and by tradition Onan entered into a Levirate marriage with his dead brother's wife, Tamar, to continue the brother's line. If Onan fathered a child by Tamar the child would inherit all of the dead brother's possessions and rights; if there were no sons Onan would inherit everything. So Onan pulls out, meaning he gets to bang the widow, and still gets to keep everything -- which is pretty sleazy.
God isn't really a fan of this, and punishes him accordingly.
It doesn't, because what I've essentially explained in my example. Too much population, and you collapse the environment, and human race suffers and then dies. I hope even smart atheist progressives would realize that meaningful ways to preserve human race are things like building a Mars colony, or ensuring the Earth's ecosystem does not collapse (such collapse would likely lead to great wars, possibly nuclear).
And regarding your latter point,it is as you say simplistic - much like the proverbial bacterium on an agar plate, our growth imperative will destroy our future if we overrun the bounds of our environment. I think we will see the issue become more important as the consequences of overpopulation (with respect to resource consumption and carrying capacity) begin to bite.
But science also teaches us that humans have a set of common, shared values, and while they may be arbitrary in general, they're not arbitrary to us. And they're shared, because humans are not isolated minds, each coming to existence ex nihilo, but in fact are connected through the process of reproduction. All of us have brain architecture we've inherited from a common ancestor.
This is how science can point us where to look for some practical morality.