Yes, いなきゃ is conditional. で indicates cause/reason there. いないのが理由/原因で makes more sense?
It's often, or more likely always set with いたらいたで(うるさい, わずらわしい, 邪魔になる or other expressions of negative nuance).
(If you're here, you annoy me because of your presence, but) if you're not here, I feel lonely because of your absence.