osxksp64.sh

#!/bin/bash

ksp="$HOME/Library/Application Support/Steam/SteamApps/common/Kerbal Space Program/KSP.app/Contents"
unity="/Applications/Unity/Unity.app/Contents/PlaybackEngines/MacStandaloneSupport/Variations/macosx64_nondevelopment_mono/UnityPlayer.app/Contents"

transfer() {
  # Take an optional destination argument in case the destination file has a different name.
  if [ "Z$2" != "Z" ]
  then
    dest=$2
  else
    dest=$1
  fi

  mv "$ksp/$dest" "$ksp/$dest.bak"
  cp "$unity/$1" "$ksp/$dest"
}

transfer "Data/Managed/UnityEngine.dll"
transfer "Frameworks/MonoEmbedRuntime/osx/libmono.0.dylib"
transfer "Frameworks/MonoEmbedRuntime/osx/libMonoPosixHelper.dylib"
transfer "MacOS/UnityPlayer" "MacOS/KSP"

Script from reddit user aperlscript in this comment:
https://www.reddit.com/r/KerbalSpaceProgram/comments/3gcltc/64bit_ksp_on_os_x/ctxefw5

^ for bonus points you shouldn't run the backup mv twice if the destination file already exists so that if you run the script twice it doesn't overwrite the backed up files.

should also probably use \mv and \cp` to bypass aliases and be explicit about your preferences for -i and -f arguments... (mv -i would be one way to avoid overwriting, but that being the default behavior of the shell is dependent upon the user's aliases).