How do carbon fibre road bikes handle rough conditions? I'm considering buying a entry level road bike for around 2000€. 

I'll use it for commuting every day 20km and for long rides up to 150km. 

I'll try to use an older bike when it rains, but I'll have to ride the new one sometimes. Also, on my longer rides, I can't always find a road and will have to ride on unpaved roads or even some gravel.

I'm interested in some models like the Bianchi Intenso Centaur 11v, Canyon CF SL 8.0, or Stevens Izoard Pro, and I'd change the tyres to Continental Gatorskin 700x28.

Will occasional rides in those conditions destroy such a bike? My worries are not so much about comfort, but losing such a lot of money because something gets broken if those bikes can't handle it. 

I currently ride a steel single-speed bike with the mentioned tyres, and I haven't had big issues in over 4000km with some bad weather with a lot of unplanned unpaved and gravel roads.
Carbon fiber road bikes are generally perfectly capable of being ridden on less than perfect surfaces without sustaining damage.

Obviously you want to avoid large obstacles such as potholes, rocks, kerbs etc.   

28mm tires are definitely a good idea. Depending on how much poor quality surface you plan to ride on, you might want to consider looking for a 'mild' gravel bike that can take 35mm tires.