Hi,
I have a A207 (E Class convertible) with a factory fitted AMG kit, from looking at the EPC it would appear that mud flaps are available even with the AMG kit fitted, so might be worth checking with a dealer to see if they are available for you're model if you would be happy with mud flaps as an option.
On my CLS 55 from the factory they fitted a transparent film at the bottom of the rear doors in front of the wheel arch, and I believe there is a 3M product that could be fitted in the vulnerable areas of the paint work to protect against stone chips etc.
I am having the front bumper painted on the CLS and I have enquired about getting it entirely wrapped in this protective film after paint to stop the dreaded stone chips.