An icchantika is, depending on translation, often considered a person who actively hinders people's achievement of enlightenment. So your dharma towards them would probably not lead to unfavourable karma, because your dharma would benefit other people's dharma and potential attainment of enlightenment. Also keep in mind with certain sutras the moral polarity of your dharma is quite fluid, and not hard and fast codes that must be ascribed to in their totality (e.g. Hammurabi's Code of Laws, etc).
An analogy could be putting a murderer to the firing squad. You transgress them because the sum total of their transgressions would be larger.
P.S: I am not pro-killing people, I'm just trying to put forward a potential explanation for that sutra.
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