Cornerstone does not yet officially support Kaleidoscope 2, so to work with the latest beta of Kaleidoscope 2 (Build 99 and up) here is how to get set up:
Follow the instructions here Cornerstone External Compare Tools under the heading Custom Compare Scripts
The custom scripts contents should be
#!/usr/bin/env bash /usr/local/bin/ksdiff --partial-changeset -- "$1" "$2"