Você poderia fazer algo assim:
# make bash function to do conversion and deletion
conv() {
/Applications/Mkvtoolnix-7.0.0.app/Contents/MacOS/mkvmerge -o "${1%\.*}(1).mkv" "(" "$1" ")" "(" "${1%\.*}.srt" ")"
rm "${1}"
}
# make conv function available to xargs
export -f conv
# recursively convert every .mkv file in current directory
find . -name "*.mkv" -type f -print0 | xargs -0 -n1 -I% bash -c 'conv "$@"' _ %