I have seen it work both ways. Once, I had triplets in my classroom even though there were four classrooms of third grade.
I am friends with twins who have the same age children. They have always asked to have their children in different classrooms until this year because they specifically did not want one teacher and they both wanted the other teacher.
You will just need to ask, at the end of each year, for the girls to be separated. But, I don't think it is a huge deal either way. The triplets I mentioned earlier all did very well and had their own friends.It's really going to be how you handle the situation which will determine how the girls feel about this.
One last thing, don't go barging into the school angry. The school obviously did not know what the situation was, as the teacher has already said. The school may be able to change their classrooms but probably will only do so if they feel their backs are not to the wall.