You don't have to delete the file. You can rename it to something. As soon as the file is renamed to something else (just add a single character at the end of the name of change the file extension by adding a character) then launch the game. The launch window appears and goes away but the game does not launch. It will still be in the process list as user42336 answered. Then rename the file back to original and it will launch just fine. This does put it in windowed mode. BUT it doesn't really funciton as windowed mode well. You can ALT+TAB out of it and have mouse just fine without a fullscreen blink and all that. But if you go back into it, well, it reverts to fullscreen. There's no actual WINDOWED mode support for this game. There could be some others ways. This was the first google result and it was answered well just not fully nor with enough credit.
One of the things I do is write a batch file with something like this:
ren "C:\Program Files (x86)\Steam\steamapps\common\Assassin's Creed 3\DataPC_DX11.forge" DataPC_DX11_.forge
"C:\Program Files (x86)\Steam\steamapps\common\Assassin's Creed 3\AC3SP.exe"
::Begins check for Start
for /f "tokens=1 delims=," %%a in ('tasklist /fo csv ^| find /i "AC3SP"') do (set bw=%%a)
if %bw%==blank (goto start)
::Waiting for the process to actually fully launch you may have to increase the -n value if it takes your computer longer to launch the game
ping 188.8.131.52 -w 1 -n 10 > NULL
::renames back to start game once ac3sp starts
ren "C:\Program Files (x86)\Steam\steamapps\common\Assassin's Creed 3\DataPC_DX11_.forge" DataPC_DX11.forge