Is it wise to kill an insect just because it is bothering you
Damaging crops and infrastructure eventually leads to damage to humans. Worry about the karma you are creating by not helping a human in need. The amount of karma from killing an insect, even thousands, is inconsequential compared to the karma for harming one human, much less killing one. As Swami Vivekananda has pointed out, we are surrounded by life, just the act of taking a breath of air kills thousands of bacteria. Ramakrishna Paramahamsa used to kill lice in his bedding.
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