The patch knows when you used a cracked .exe or not, if you use a cracked .exe then it won't detect your game, so you need to use the original Crysis2.exe
What you need to do to get the game running on patch V1.2 + multiplayer:
1: If you haven't backupped the original .exe of V1.1 patch, then you need to put the original Crysis2.exe of V1.0 in your directory.
2: Patch the game to V1.1 again for original V1.1 Crysis2.exe
3: Run the game to patch it to version V1.2
4: Apply the multiplayer crack for V1.1
5: Run the game and be happy, it all still works, except I don't see other players chat when playing a match, for the rest it all works.
Enjoy!