>>360679>Wouldn't expense/difficulty be moot at that point?
Not really, since you're missing all the doctors, surgeons and infrastructure needed for the treatment needed. Orca itself isn't big enough to handle a bunch of births, let alone raising children that'll need multiple surgeries. At some point you'll need to find (which is unlikely) or make a hospital someplace else to handle the births and the surgeries whenever you need it.
Not only that, but you'll have to supply said hospital with all the tools needed for the births and surgery treatments and since all factories and production are gone, you'll have to start from zero even if you have the know-how of said tools. And before all that, you'll have to search for the resources needed to develop said tools. And the worst thing, you'll have to secure said place from iron worms which would be literally impossible (hence why Orca was created).
And all of this would happen while you're still fighting the IW menace, where the only resources you have are being used in Orca to keep fighting IWs. If the commander went full breeding mode then said resources would be halved at best and redirected someplace else, meaning less resources for Orca and most likely dying at some point.
In short, going full breeding mode would be a logistical (and literal) suicide. That's why Doctor and company are researching a new way to get by the origin dust problem with mixed babies, without the need of several surgeries. Making it more effective and efficient using less resources.