I was in the opposite position this past year, my daughter was in class and on the bus (same seat) at her same aged friend. It was GREAT for this other little girl because she is extremely shy and needed the "friend".
However, as the mom of "the other kid", I was VERY happy this year when they weren't in the same class. I felt like the shy child held my daughter back. She was very clingy and would cry to her mother if my daughter didn't play with her one day. The other mom would call me and ask if anything was going on...so I'd check with my daughter. My daughter would say, "No Mom! I just was playing with Susie and she didn't want to play with us, so she sat down and didn't play with anyone!"
Although I felt bad for this shy little girl I didn't feel it was fair to force my daughter to play with her everyday on the playground. It's not like she was being excluded, but she was SOOO shy she wanted to have my daughter all to herself, and if that didn't happen, she just wouldn't play at all.
This year has been great for my daughter AND her shy friend. The shy friend has learned the difference between being shy and being excluded. She has made many new friends, and so has my daughter. They are still very close, but at least they're not bound at the hip anymore.
I think the best thing you can do for your daughter (and her friend) is to create some separation. See if you can find out from the teacher some of the girls that are going to be in class with your daughter next year and see if you can schedule some playdates with them over the summer or even get her onto a team sport with some of them. I know for us, Girl Scouts has been a great way to make friends from our school, but not necessarily the same class. That way our girls always seem to have "a friend" in class. Then they can all play together at recess too.
Finally, I think that it's critical to teach your daughter how to make new friends, and how to start getting over her shyness. By protecting her, I think it's akin to sheltering her. She has to learn to open up, say hello and make new friends. This is part of life! She's not a baby anymore. By third grade, I think parents "requests" for the classroom assignments should be limited to learning issues or bullying issues.
Best wishes!