My view is they established a pattern where you always have to make room for stuff before you can replace it (tomes, items). There are one or two exceptions, like squadron members, but I believe even there you wouldn't be able to replace a member if they were out on a mission. Leaving stuff in the care of mammets has clear limits. You likely wouldn't interact with anything in their care otherwise (be it crops or animals), so I don't see how it's a failure on the dev's part to not allow you to replace an animal in care. Again, I said they could probably use a little more clarification, but that's it.