Pros

1. Spaying a rescued pregnant cat will help contain the overpopulation problem. There are simply too few homes for the huge number of homeless cats.
2. Spaying a pregnant rescued cat will help prevent the deaths of living cats and kittens. Even though a pregnant female cat might be adopted by the finder, with good homes waiting for her kittens, each of those kittens will indirectly be responsible for the death of a shelter cat or kitten that might have been adopted into one of those homes.
   A case in point is a rescuer who also fosters cats, with space limits to her ability to house them. She recently had to make a choice between spaying/aborting a pregnant cat that had been dumped on her doorstep, or sending a litter of kittens she had been fostering to the local shelter, where they would have immediately been killed. So for the "greater good" she had the new cat spayed, even though it cost a lot of emotional pain.
   

1. Very young cats and very old cats rarely enjoy the kind of physical condition that would warrant allowing them to give birth. Birthing and nursing a litter of kittens would easily take their last ounce of strength, and could kill them. This truth is even more evident in the case of pregnant strays, who may have already borne dozens of litters of kittens. (A female cat is capable of bearing at least three litters of kittens each year.) The kindest and most compassionate action anyone could take with one of these cats is to spay/abort her.
2. The only time a pregnant stray cat should be allowed to give birth is in the case of being near-term. There is a Roe vs Wade aspect to this argument, which brings up a whole different issues of viability - "when does it occur during pregnancy?"

Cons

1. The taking of life, whether it be human or animal, already born or a fetus, is immoral. There are no "excuses" that make it all right.
2. Shelters and rescue organizations are institutions, and their primary concern is the movement of cats out, to make room for those coming in. In that sort of atmosphere, moral considerations may take second place. However, an individual who is willing to keep both the mother cat and the kittens or find good, permanent homes for them, should not be made to feel guilty for allowing the birth.

1. Where is the evidence that the people from the "good homes" might have instead adopted cats from shelters? Perhaps they weren't even looking for a cat until they heard a friend, neighbor, or co-worker had adoptable kittens. (In response to "pro argument" number 2.)

Where It Stands

There will never be a complete resolution to this issue until cat owners become responsible caregivers, by spaying and neutering their cats. As more and more kittens are born each year, more and more stray cats will appear, and the feline overpopulation problem will increase exponentially. That is why this issue is just a small part of a greater issue: Spay and Neuter.