The use of dividers has been discussed here several times before. With movable partitions the specific models and the details of the construction can make a tremendous difference. However, unless it is just "normal" level speech from both groups for that large a space it is likely be very expensive to provide adequate sound isolation. A operable partition will almost certainly not provide sufficient isolation for two groups of 300+ when one or both are likely to be using higher level, full range music. And don't forget sound isolation for classrooms, you may have a lot of running and yelling in one and want a quieter space next door or may have high school or junior high youths discussing issues you don't necessarily want younger children in the adjacent corridors or rooms hearing.
You would also have to have a sound system(s) that served each space as well as the combined room, which will increase the costs and complexity there. If the room has multiple possible subdivisions you may end up with multiple systems. The same concept applies to lighting as well.
Providing a good acoustical environment for the whole room and then also maintaining good acoustics for each of the smaller divisions will much more difficult and will require significant additional effort.
I'm sure that others may share their personal experiences and comments, but you really need to get a qualified and experienced audio, AV and acoustical consultant(s) and/or integrator involved early on. I recommend that they become involved either as part of the Architect's design team or at the same time as the Architect. Not getting these parties onboard early enough can result in wasted effort by the design team and additional costs and/or compromises for you.
From experience it is also good to get the design professionals involved early on to address the concepts the church develops. It is great for the church to start identifying, developing and organizing their ideas, goals and needs as early as possible, but without some immediate input on how these could affect the construction and budget they can later become problems. Too many times people get focused on specific items or goals without really understanding the impact and when that is later found to be impractical they become disappointed or end up making compromises elsewhere to get something that isn't really that important except that they have become focused on it.