Is it permissible to name males "Habib" despite its prevalence among Christians, even though companions were named by it?

There is no harm in naming someone Habib. Its prevalence among non-Muslims does not prohibit naming with it. Only names specific to them are prohibited. Ibn al-Qayyim divided names into three categories: those specific to Muslims, those specific to disbelievers (which Muslims are not permitted to use), and those common among various groups (which no one is prevented from using).