Mrs. Mann's punishing the orphans when they ask for more food has less to do with discipline and more to do with covering up her own embezzling. She takes for herself some of the funds allotted to the upkeep of the orphanage. The last thing she needs is an orphan calling attention to their lack of nutrition by asking for more food.
The orphans are also guilted into silence, even by the officials outside of the orphanage. Later on, when Oliver is brought before the Board, one of the gentlemen present tells him, "[I hope] you pray for the people who feed you, and take care of you, like a Christian." The men of the Board accuse Oliver of ingratitude when he betrays the least bit of misery. When they learn Oliver has asked for more food, one even suggests he is doomed to become a criminal when he grows up—he must be greedy if he wants more.
When Oliver asks for more food, he is indirectly calling to attention just how bad the orphanage is. His request not only puts Mrs. Mann in danger of being prosecuted, but it also criticizes the state for its treatment of the unfortunate. This is what leads to the overreaction from the adults in charge.