On the contrary. Our schools routinely split up best friends so that kids have to come out of their shells and so they don't become cliquish. We had about 8 friends on the street who were going into 5 first grade classes. We asked the school to split them up, and made it clear we weren't requesting teachers but just asking that kids be split up. One teacher actually lives on our street, so we suggested that they ask the teacher if she preferred to be assigned kids who lived at the other end vs. those just a few doors away from her.
School is about school - it's not about play dates. My guess is that the friendships are too dominant and they are a problem, and so the teachers split these 3 kids up on purpose.
The only way kids will become withdrawn and shy is if parents make such a big deal about this that the kids think they will not fit in with the new kids. The message MUST be, "You made friends in kindergarten, you will make new friends in first grade. You will continue to see Susie and Ashley on the playground and at play dates, and if your friendship is strong, it will survive separate classes."
I respect your prayer tradition, and will share mine: I don't believe that God micromanages our lives to the extent that God oversees class lists or lottery tickets or whether we get a cold or not. I believe that religious people pray to God for strength and guidance in handling challenges. If your daughter wants good friends, she must be a good friend to all - perhaps this is an opportunity that God is giving her, and perhaps God is confident that she will excel in multiple friendships.
If you think she will regress, then you talk to the teacher in September about perhaps being a little extra nurturing or putting your daughter with a giving and warm child in the same seating area. But meantime, you work on building your daughter's confidence and not at all on how awful this is. Your daughter has come out of her shell - that may be due to maturation and abilities, not just these 2 friends.
Please, please, don't handicap your child by making her feel incapable of making more than 2 friends for her entire life. If she is a good student (in terms of making an effort, not in terms of her grades) and a cooperative classmate, she will attract lots of friends. Please help her grow to believe in herself, and don't let her absorb your anxiety and fears.