Do you have a budget? Do you want to shoot flash or would you rather work with natural light?
Iwould look at options from Canon, Nikon and Pentax and consider some bright prime lenses (aperture of f1.8 or less) or fast zooms (aperture of f2.8) to allow as much light in as possible so you can get good exposures in the dim lighting we call find in churches.
I'm fortunate that our church is well lit with large windows on all 4sides even so it is not great.
Shooting flash can be difficult as the ceilings are generally high and you can't use bounce flash so you have to go direct if you are not using fast lenses which can make harsh lighting.
If you let us know more info we can give some advice to help you hone down your decision.