Neither is better. They are both better for their own reasons that cancel out. The skill level of the players is the same on either platform. As someone who played CoD4 extensively on both 360 and PC, I can attest to this. While the kb+m combo is much more accurate and easy to use for aiming, I still prefer the controller because I just think it feels more natural than using my left hand to press keys on a keyboard for movement. As to his argument about controllers being tougher, he is on the right track, he just didn't expand upon it very well, or you didn't include all of his arguments. Dual analog is much more difficult to use than a mouse for aiming. It requires much longer practice to master your sensitivity level. The unfortunate downside to this is that developers think they need to add auto-aim on consoles. I absolutely hate this feature because it is ALWAYS messing up my sniping on CoD4 when players are running in front of my aiming reticule.
Now, I'm not saying console players are more skilled because their input device is harder to master. The players on either game are equally skilled. I am the top player on either platform when I play, and I see no difference in skill level of others. If you take the best players on consoles, give them time to adapt to kb+m they will be just as good as the best players on PC and vice versa.
Oh, and just to try it out, I used a program called X-padder (I think) to map my 360 controller for CoD4 on PC, and while using the controller I was still in the top 3 players. The only problem with the controller was that when looking down the sights, there was no change in sensitivity like there is on console, so I was not used to that and it ruined it for me. If they could make a good "half" controller for the 360 that I could do movement with a controller and aiming with a mouse, I'd die a happy man.