Can I delete main account and use only the secondary account?

If you are talking about a Facebook page or group for your church, that group or page needs an administrator. That's you, your private account. You can adjust your privacy settings on Facebook by clicking the gear wheel in the upper right corner and following their directions (I won't post them here as Facebook tweaks this all the time).

If your parishioners have an issue with it, make sure to tell them that the private account is for you as an individual, whereas the church group or page is for church business. But don't be surprised if people still want to reach out to you directly. They may see it as being more private or more likely to get to you.