Via the purchase contract the breeder gets to decide that. Buyers options are to follow contract, negotiate terms, or keep looking.
Wow, call me naive! I wrote a letter to the breeder of our chessie asking permission to use the name! I am proud of the dog and his heritage and certainly wanted to acknowledge the breeder's efforts. But I agree, the answer to the original question is just ask. I bet any of the respected breeders would agree that if you don't want the name, there is no need to push it. I bet most breederrs would still sell me a pup as long as I promised to provide the best life for it and had every intention of some sort of competition. Even if I wanted to name it with my own kennel name even though I am not and never ever intend to be a breeder.
We bought a 3k pup last year from a very good breeding. The kennel never mentioned using their kennel name and we had no contract other than my deposit to hold a pup. After receiving the pup we had to make numerous phone calls to receive the registration papers. When the papers did finally show they had already written their kennel name in the box?? I made 2 calls to the kennel about this as we have our own name and wanted to use it. We never received a return call and I figured since this was not mentioned via contract or verbally I went on line and registered with my name, especially after spending 3k.
Using a breeder's kennel name is a good way to be able to track down where a dog came from when doing research on pedigrees, etc. It also helps to "honor" (so-to-speak) the breeder for producing a fine specimen of the breed. To me, removing the name when obviously the breeder prefers it is used (having already filled it out on the registration forms) is like a slap in the face to them. Not something I would personally feel comfortable with after they have trusted me with one of their pups... If you purchased your pup from a breeder you are proud to have a pup from, why would you not be proud to display their kennel name in the registered name of that pup?