Eye ointment after birth

Has anyone given any thought to the eye ointment that is administered after birth? It wasn't really on my radar, but my midwife got talking about it yesterday. While it's legally mandated where I live, she said she would support me if I wanted to opt out, especially as I've been tested for gonorrhea and clamidiya and am in a long-term monogamous relationship. She told me she wouldn't do it if it was up to her (and neither would a growing number of Canadian pediatricians based on recent public statements). So now I'm wondering if it isn't beneficial to expose a newborn with a developing microbial community to unnecessary antibiotics. I'm usually supportive of medical directives, but I'm concerned this policy is no longer based on sound science. Has anyone else struggled with this?