Hi, Dave. Pet stains will usually bleach out of a hardwood floor pretty well and should be less noticeable than new wood. I would say that replacing the boards should be the last option rather than the first one. It would seem to be more logical to work with someone who says "You have stains and I might or might not have to replace the boards. I will try to save them but I want you to know this ahead of time. If I have to replace. It will cost $XX per board."
The sanding should remove what the bleach doesn't get but I hasten to add that without seeing the stains and maybe sanding a little to check the depth, no one can give you a sure answer to whether they should be replaced or not. If they have to be, the floor people should be able to match the new wood in pretty well.