I've gone from an 2003 MCS to a Cooper Clubman, not exactly the same comparison that you are looking for, I miss the out and out performance of the old s, then again the increase in space and more civilised ride makes up for that. I've also driven a D as well, to be honest the difference in performance between the two engines is not that noticeable, though the petrol engine does have to be revved a little to get the best out of it.
I've put 17" wheels on my car and in no way does it handle as well as my old s, it seems to be more prone to bumps on the road (especially going around bends, which can be quite unnerving) and it feels far more vague. I wouldn't even consider sports suspension as well, the only thing it might do is make the ride far more harsh.
My advice is that you should look at both models and not just the D, I really wanted a D, based on road tax (£25 a year from next year?) and the MPG but after looking in more detail the extra cost of the D over a petrol made less sense, I drive through a city to work each day and I doubt there would be that big a difference in MPG (About 10 MPG urban at the most).
Also you can get a good discount on a petrol Clubman over the D, expect the real difference in price is more like £2k not £1k, that's a lot of petrol and road tax you could buy over the life of the car.
Then again the trade in value of a D should be rock solid and if you pay congestion charges the D might be the better choice
