A very interesting project Panos. I had also invested in two of these churches, with the idea of using them as a "Cathedral base" for my crusaders, but hadn't considering painting them...yet.
The holes sadly do detract greatly from the "finished" look, and this is one reason I prefer Steck to System X. The gargoyle idea would work well for the outside walls, but what about the inside holes?
Much as I dislike the newest clip system for its inability to be customised or deconstructed, it does at least do away with most of the construction holes. Of course Steck did away with ALL the construction holes, so once again it's the superior system for finished looks, as well as adaptability.