Something similar happened to us, though at a slightly older age (already-early-entered child skipped from 3rd to 5th grade), also in a small private non-GT school. Except we didn't find out that the school had done a unilateral grade skip (within the multi-grade classroom) until I saw DC's schedule in the backpack after the first day of school.
We let it unfold, and ended up having good social and academic outcomes, including additional school-initiated multiple subject accelerations. I actually think you have an even more promising situation, since I agree with spaghetti that you have the potential to have a little cohort move forward with her.
