Usually at Shiloh, just direct your divisions past the skirmishers, they'll fall back. But they become P.I.T.A.s on the other side of the creek. I usually assign a brigade to wear them down.
On a different note, infantry, skirmishers, cavalry, and supply wagons all surrender if circumstances fall in place. The only organization that never surrenders is artillery. It would be nice if they would eventually surrender as well.