Well, certainly masonry is sometimes modeled as a continuous medium system, and then some significant results can be extolled from such analyses.
A more detailed analysis of this structure will require complementary studies through masonry design procedures.
Restricted to your intent, first to comment that maybe other FEM programs more competent in dealing with solid elements may be more suitable to model massive structures like those of churches. Whatever the software one uses, maybe the biggest challenge is proper adjudication of the loads to the standing structural system. Your church has some apparent configuration, but surely as well hidden features. So, as your first task, gather everything you can about the plans and actual structural configuration of the church. The roof system is always a challenge because it has the inner vaults over it and can have quite variegate arrangements of woodwork to conform the outer roofs, all loading in a priori unknown strong points, till one identifies them. Also, arches and vaults are sometimes intently loaded at the bottom with loads of earth or other stone work to compensate otherwise flexural action at the kidneys of the arch etc (centering the push line in the arch section). Unloading (sometimes asymmetrically) the arches of this corrective loads has caused ruin.
So, first recommendation, use 3D solids (and better more clement programs for that than SAP2000). For modulus of elasticity it is usual to take 500 times the average compressive strength of the masonry (squashing without any buckling). Then place correctly the loads. Then your main interest will be the deformations (to see if small) and the principal tensile stress.
Masonry only accepts very limited tensile stress (and that if cemented). Even if averaged some take 10% of the compressive strength as limit tensile stress, locally you may be getting cracks with tensile stresses under 1 kgf/cm2. A more reasonable limit tensile stress for cemented masonries will be 2.5 kgf/cm2, look references for these things. Look also to the shear capacities of line members like arches etc if you use them but solid with principal tensile stress uses to cover for such phenomena, at least as an informative tool. For flexural action the worse principal tensile stresses will appear at surfaces but axial and shear forces may origine that the worse principal tensile stress is sometimes within the mass of the solid element; so make inspecting cuts for the stresses.
Model correctly the soil, with long term effects if you need to ascertain the future of the masonry structure; in any case, consider the soil properties to gauge their effect on the structure.
Once you are satisfied with your preliminary investigation, delve in more detailed masonry structural analysis trying to see if buckling, instabilities from push, or localized wind effects put in danger particular elements in the structure. ... Hope that this helps.