It can always be difficult in an amateur production to figure out who is
in charge. The director should always have the final word on the drama,
but in a church there are many other considerations. The music director
has control of the music and choir, the senior pastor has final say on
any theological question, even the custodian may have a say on what the
set can look like (for fire code reasons maybe).
It can be frustrating juggling these competing (sometimes) authorities.
Focus on the acting. Focus on what is under your control. Make that the
best it can be. Try not to worry too much about the other stuff.