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.
Cellular components are also susceptible to damage by physical stress.
After all, they are living cells. With mother's milk, you get at least two functions for the price of one. With manufactured formula, you only get the individual beads, never the necklace or bracelet. And never the living cells. So, please handle human milk gently, respectfully and kindly.