We've had the Cooper SD All4 with the 6-sp manual now for almost a year (Nov 2011 build) and the gearbox is good as gold. No issues with the clutch or gear-change system.
For us the auto was a non-starter too due to the major impact it has on fuel consumption (cost was part of it too). I only have the auto on my X6 because there is no choice!!
I've also been a firm believer that small engines & cars are not best suited to auto's anyway. And the Countryman isn't that 'big' either - it's based on a 1 Series after all.
I would not want to do a daily commute in heavy traffic in a manual now - automatics do make that job much simpler - but as I rarely do that the manual for me was the only way to go. Of course when I started driving 30 years ago, autos were very rare and we all used to sit in London traffic stirring our manual gearboxes.......
I suspect the clutch issues in the article are 'one of those things' and just might have been exacerbated by the car going through a number of different drivers and driving styles. The first driver may not have had a good 'clutch habit'.....but it's all speculation.
We have a 2005 E46 (3 Series) and that has always had a dreadful 1st to 2nd change. BMW said there was nothing wrong, but that box has been bad right off the bat, and only that specific car is affected as we've had and driven other BMW manuals as loaners with no issues at all.
My 2005 X5 auto gearbox destroyed itself at less than 42,000 miles when a 50pence part in the torque converter broke!! Just bad luck where the bits ended up as they blocked the oil pump and that was that - although that box is now 'known' to be a weak area with more and more owners having to replace/rebuild them - a Ł2k bill for most (Ł7k from BMW though!!).