Actually, pretty sure PC versions have different fireing caps, because anyone can max them with a mouse really... The COD 4 PC version certainly feels different in that respect. Also, the auto aim is pretty much non-existant, aiming is actually really hard with a joystick.
Aiming with a mouse is a full arm movement that involves shoulder, elbow, wrist, and fingers... that really reduces the need for aim assist because we are so used to using it daily and because a thumb stick is just that... thumb movement... You are going to put yourself at a pretty big disadvantage by using a controller with the PC unless you are playing an RPG or driving a vehicle.
You CAN swap between them freely though. If you have a controller plugged in you should easily be able to use both the mouse and keyboard setup and the controller simultaneously.
Yeah, I have the wireless adapter for windows and I've been playing assassin's creed revelations and skyrim on my laptop and the joysticks are just very sensitive. It's really easy to switch back to the regular keyboard and mouse though, it's right under the options or settings in the pause screen (or the main menu) for most games.