No twist or pedels, I always have 'autorudder' enabled in the settings.
Since I have the same Logitech stick (although fully set up for force-feedback etc.) I carried out a simple test for you, simonmd - turned on 'autorudder' and tried a flight.
Guess what - the 'autorudder' setting didn't make any difference, the rudder still required twist control.
I'd suggest that you set up an aeroplane on the ground, go to 'outside view', move the stick various ways, and watch which control surfaces are doing what. I suspect that you'll find that sideways movement of the stick (which would normally produce rudder movement on the ground, if you were using a two-axis stick) still actually moves the ailerons, because you're using a Logitech. And that you have to twist the Logitech to move the rudder, whether or not 'autorudder' is turned on.
I think that what happens is that FS9 'recognises' the Logitech and treats it as a force-feedback anyway, regardless of the 'autorudder' setting. And the stick itself automatically profiles itself that way.
The best solution would probably be to use the Logitech as it was intended (after all, you paid money for it!). You don't often need the rudder in flight anyway, and the twistgrip is much better for manoeuvring on the ground, and for keeping straight on takeoff. If it feels too sensitive, go to Controls/Joystick Sensitivities and adjust the sliders till it suits.
The next alternative is probably to get a cheap two-axis stick and use that instead, with 'autorudder' set.
You MIGHT sort the problem out by turning off the power to the Logitech and checking in 'Settings' to make sure that the game no longer 'recognises' it. But I can't see the point of that, it's wasting the stick's other capabilities.
Whichever route you choose, make sure to calibrate the joystick regularly.