Lactoferrin, lysozyme, and other protective components work their protection magic when they are in their original shaped molecular structure.
Some components remain intact, even during freezing, shaking or heating.
They not only protect the gut from many kinds of infection, but also prevent inflammation of the gut lining. Even broken up, the separate amino acids are still really good stuff and are digested by the baby as nutrients. Imagine a set of pop-beads assembled into a necklace or bracelet. When the beads are acting as a bracelet or necklace, they are doing their job as protective elements. When you break apart the beads, you have in your hand many individual chunks of amino acids which are then digested.