I get what you mean. I've always been a cat person, looked after female cats to be more specific. Each one of them was desexed. You've triggered me to think back to when I also had feelings about this. A few questions I recall: Does an animal mourn in some way, not being able to have their own? Do they sense their inability to produce? Is this right or is it kind of arrogant for humans to do this, in this way?
Although it doesn't seem fair somehow, I can make better sense of it now. If cat's or dogs were in the wild they'd function as nature intended, keeping in mind that nature can be harsh in many ways, with predators and such. They'd produce multiple offspring as often as possible, to increase the chances of a handful of offspring surviving. Being so well cared for by us, I suppose we have to act like nature to some degree, provide some form of animal control (of numbers). Whether it's the right kind is a whole other story. Before medicine and care became so advanced in this world, people also had less of a need for birth control, based on such low survival rates in infants. Now we do.
The connections we make with creatures/creation is so important, giving us our connection to life. Whether it's a person, an animal or a tree, all thrive on what we give to them and what they give to us (what we share). I imagine you'd agree that it's a lack of sensitivity that generates a disconnection in life. While my sensitivity challenges me at times, I couldn't survive without such a connection.
I hope your little pup recovers well. She's lucky to have you in her life :)