I would not have a problem with them staying together. It sounds like they have a special friendship. Who knows, something could change by the end of 3rd grade as well.
My concern would be if this best friend is your daughter's ONLY friend.
I am sure that is not the case here but if it is, your daughter needs to be in some programs outside of school to socialize if she is not socializing with others at school.
It is good to have a best friend but we need to have many friends. As she goes through her school career, she will need to know how to work well with others.... girls, boys, children of different races, etc... hence.. being diverse. Especially in the higher grades you deal with study groups, project groups and it is important to have communication and social skills so each person can pull their weight in the group situation.
Just my two cents. Have a great day!