Can Repetier host run a multi-material printer such as the Prusa i3 MK2S?
Yes, it can. I have configured it for as many as four extruders. The problem may be in the slicing, as the slicer is responsible for generating the tool change commands.
One problem with the Repetier multi-extruder support is that, although the temperature of each extruder is reported by the RepRap firmware response, only the selected extruder is updated, and only one extruder is shown in the temperature graph.