My question refers to the twelfth blessing of the Amida, which seems to contravene the Biblical mitzva of ahavas yisroel*:
"And for the slanderers let there be no hope; and may all wickedness perish in an instant; and may Your enemies be cut down speedily. The wanton sinners -- may You speedily uproot, smash, cast down, and humble speedily in our days. Blessed are You, HaShem, Who breaks enemies and humbles wanton sinners."
According to my siddur (Artscroll), this originally referred to "heretical Jewish sects" such as the Sadducees, and also refers to heretical influences today. I may not know my history, but to me, the Sadducees seem no "worse" than karaites; and in any case, does it really matter? We are supposed to love our fellow Jews regardless of their faults, perceived bad influences, and differences with our opinion, then and now, no?
So how does praying directly to G-d to have them "broken," "smashed," "cast down," "cut down," etc., fit together with this essential concept?
(*Relevant mitzvot and sources: #26, and possibly #34, on the list here.)