The cruelty is born of the fact that its being born of the sentiment of "Tough Luck kid. I know you're going to grow old and die, but I want to experience being a mother." Also, as you point out immortality is an unnatural state which is another reason why Kiyomi made not having children a condition of maintaining it. You state that having children is a biological imperative, but the simple truth of the matter is we can and do choose to follow it. And yes I do believe that given the choice between potentially living forever and having children they would choose to live forever.
You see that Naruto might come to resent the child, but I think the opposite might also hold true should the child be born but not be immortal. You point out that their response should simply be sorry but it's not a natural state so tough luck kid. But don't you think a kid would resent the fact that he or she was born without such a gift. Plus, if being immortal is outside of nature, which I agree it is, then why would they still feel a drive to have future generations. That need to have your genetic material passed on is born of the fact that they do have mortal lives. But with the fear of death, mostly removed why would they still feel a need to have children? Furthermore, your entire last sentence is exactly why I don't think any of the women would choose to give up being immortal to have a child. One the man they are with has made his desire known that he isn't interested in having one. Two, their current situation is living a lifestyle of sexual indulgence which a child would throw a monkey wrench into. Three, as the other women continue to enjoy their happy Harem lives, the woman that chose motherhood would be changing diapers, and taking care of it as it grew.
You also describe it as stealing her youth and robbing her of eternity. But the truth is that she willingly gave them up. That is what making a choice is, do the two results necessarily have to be equal. No of course they don't which is why sometimes its easier to make a choice? Would she potentially come to regret choosing to have a child? Yes that is indeed a possibility. But that is why there should be consequences for making it. By making there be a heavy consequence it does make a person consider the results of making it. That to me is the difference between a person that lets their instincts rule them, or who is guided by intelligence.
Finally, in regards to your last sentence everything you laid out is also exactly why I think the women would choose to remain immortal rather than have a child. Having a child is an unknown proposition, it's what's behind door number two when you already no what you have behind door number one. Will some people still take what's behind the second door? Sure, but if you know it leads in death while you can enjoy eternal life with what you already have, I don't think anyone would find it a tough choice to make. Kiyomi weighted the choice so that the women would choose door number one. You might find that unfair, but as you point out in your reasons life isn't fair, and as the one granting the ability she is also the one that gets to set the price.