It could well have been someone connected to the church and I concede it's possible that they met at the church building to go somewhere else, but I highly doubt that the church itself was the crime scene.
An active urban parish would have quite a few people coming/going from the building during the day: for Daily Mass, to pray in the sanctuary individually, for pastoral counseling, church committees, etc. Most urban parishes typically have at least 2-3 employees around during the day, sometimes more (1-2 priests, a parish administrator/secretary, possibly a director of religious education, maybe a deacon or nun working on outreach ministries, plus any musicians or janitorial staff who might drop in for specific purposes). In short, unless it was a dying parish, a Catholic church would not be a great place to hide a body even temporarily.
Also, based on what has been reported about the Jolkowski family, I would venture a strong guess that they reached out to people at the church in the immediate aftermath of the disappearance. So even though it took police 10 days to start investigating, people at the church were likely clued in before then that the disapparance had happened.