As a general rule, you NEVER want to have a taxi wait for you if it's going to be more than just a VERY quick stop, or if you're going to some VERY out of the way rural location. Let me just make up some phony numbers to illustrate a point. Let's pretend the taxi will cost you $20 to get to the church. It would cost another $20 to go back to WDW. You should not also want to pay a driver for his time to sit and wait for you while you're in church -- that could be another $20! I can't imagine it will be too difficult to get a taxi at the church, and if there are none there I'm very sure someone there would be more than happy to help you out and call one for you.
I hope this wasn't too confusing. The point is, unless there's a VERY STRONG reason why you want to pay someone to wait for you (such as being far away in a remote rural area), don't pay someone to wait for you. Put another way, think of a taxi as a RIDE from Point A to Point B (a one-way trip), and don't think of a taxi as a car that you're hiring for a day or a portion of a day.