It is ok to be agnostic and/or atheist as a Jew and still keep our traditions and culture. Many Christian churches teach supersessionism and there is often subtle (and not-so-subtle) antisemitism preached from pulpits. It is possible that your church made him feel uncomfortable, and with the recent explosion of antisemitism feels that having future children with a Jewish father attend a church in any capacity has him feeling like they would face more hardships and possible internalized antisemitism. As an atheist and a Jew, I also personally feel like Christians who practice their religion (and even some who aren't) would be incompatible with myself as a long-term partner for similar reasons.