As far as I know, doom3 doesn't support joysticks. I'm not sure where in the options screen you were able to enable it. I'm running version 1.1, and don't see any reference to joysticks in the menu.
I use a mouse and joystick myself. The joystick is a belkin n45 modified for one-hand use.
I've relocated the right-side triggers to under the left-handle so I get about 15 buttons without removing my hand.
The software permits the assignment of keystrokes to axes/buttons so it works in doom3. You should be able to do the same with your Saitek.
The option to reverse the mouse axis is in OPTIONS, GAME OPTIONS, INVERT MOUSE, YES/NO.