What does Haley do to Tom that upsets Mrs. Shelby and all the slaves who have come to see Tom off?

Haley shackled Tom with chains.

Tom got in, and Haley, drawing out from under the wagon seat a heavy pair of shackles, made them fast around each ankle.

A smothered groan of indignation ran through the whole circle, and Mrs. Shelby spoke from the verandah,—“Mr. Haley, I assure you that precaution is entirely unnecessary.”