What caused those colorations in bedrock?
This answer is based on a cursory look at the 1:50000 Foglio Appiano, from the Geologic Map of Italy (in Italian Language only, as far as I can tell). As I pointed out in comment, I intend it as just a start for further investigations, which should be done with more detailed geological works and possibly more field work. I'd recommend contacting the office of the Geological survey of the Provincia di Bolzano as they certainly know the area well and may be able to answer on the phone or by email.

This is what I think, based on my cursory look.

The cross section C goes ~E-W just north of the town of Cornaiano, relatively close to the location of the Church, which is just West of San Michele (based on Google map link); I indicated its approximate whereabouts with yellow circle in the figure below. It looks like the rocks in your picture could be an outcrop of the ORA formation (in orange in the figure), a Rhyolitic tuff of the Atesino volcanic group.



Also the Schema tettonico below (look for Appiano) shows the Atesino volcanic group and is in contact with a very faulted sedimentary section (Successione sedimentaria permocenozoica); I'd say geothermal fluid circulation through these fractures causing hydrothermal alteration at surface is a plausible explanation for the coloration you captured.