Cruel and sudden, hast thou since Purpled thy nail in blood of innocence? (lines 19-20)
Despite the huge stakes the speaker laid out in the second stanza, the woman kills the flea anyway. He calls her "cruel" and says her action was "sudden" and therefore not well considered. She now has the "blood of innocence" on her hands, as if she had participated in the crucifixion of Jesus Christ himself! These lines mark the high point of the guilt-trip.
Wherein could this flea guilty be, Except in that drop which it suck'd from thee? (lines 21-22)
Shifting gears a bit, the speaker backs away from the whole, "You're a villainous monster" routine. Instead, he asks the woman to feel pity for the poor dead flea. He's probably hoping these feelings of pity will extend to him, too. He's like, "What did the flea ever do to you?" To which, in perfect hindsight, we might reply, "How about being a carrier for the Black Plague, one of the deadliest diseases in human history!"