I think the distinction here is between cruelty that achieves one's intended aims and cruelty that backfires. The word "impolitic" relates to the latter part of CB's statement: "Mrs. Ferrars does not know what she may be doing -- what she may drive her son to."

Mrs. F's actions are not "politic" in that she's not achieving what she wants, which is to keep Edward from marrying Lucy; she might even drive her son to suicide (or whatever it is that CB is hinting at). A more prudent or "politic" person might have found an artful way to separate Edward and Lucy, whether cruel or not.