Absolutely, this is one request that the schools usually like to get. They would rather know, in advance, if two kids don't get along.
After my DS had some conflicts with another child in his K class, I asked the Asst. Principal if it would make sense to separate them the following year. He laughed and said that they were already on the "list". He said that they keep a list for each grade of the kids that probably shouldn't be placed together. This is apparently pretty common.