This is taken from the manual for the game, but should apply to any gamepad, not just Xbox 360 controller:
Xbox 360 Controller
SiN Episodes contains limited support for using the Xbox 360 Wired Controller when connected to a Windows computer. To map the joystick buttons:
From the Main Menu, select Options.
On the Keyboard tab, select Advanced....
Enable the Developer Console and press OK until you get back to the main menu.
Press the Tilde (~) key. On most keyboards, this is to the left of the 1 key.
When the console comes up, type "exec gamepad" (without the quotes) and press Submit.
Close the console window.
Exit the game.
The next time you play the game, the Xbox 360 Wired Controller will function.
To restore the original settings, you can pull up your Options window and select Use Defaults....
Just make sure you exit/restart the game after changing the joystick settings because the Source engine applies these settings when it starts up and can't change after that (a lesson we learned the hard way when testing