First of all, flutter echo is continuing echo regeneration between parallel surfaces. What you are experiencing is just plain echo.
The sources could be:
reflection off the pulpit
the energy from a stage monitor wedge
slap-back from the back wall of the santuary
other open mic's that pick up the pastors voice
You say you get the echo even when the pastor is not at the pulpit, so that appears not to be the problem. You also say there is no mic at the pulpit.
If you do provide monitors for the pastor while he is on lavalier, this is a BIG mistake. Unfortunately...... I know all too well that somewhere some pastors get the idea that: 1) they need this and 2) they can have it. In order for the wedge(s) to be heard the acoustic energy from the monitor(s) must be at equal or greater level than the pastor's unreinforced voice. This is the same as it would be for a singer except the singer uses a handheld cardioid mic with the monitor pointed up into the null point of the mic's covergae pattern and with the singer "eating" the mic. The reality is that the pastor does not need a monitor when he preaches or speaks. I have won this battle time and again but often it takes considerable time and hand-holding to win it.
If the problem is slap back from the rear wall, you either acoustically treat it or you see if the FOH ldspkrs can be re-aimed so that they project down onto the congregation and therefore any over-coverage gets "grounded" into the seats.
Finally, if you feed the pastor into choir monitors and the choir mic's are left on..... well, I doubt this is the problem.
Let me know if any of this helps.