I have the same problem with my wife and my C43 AMG (which is probably even stiffer than the CLK55) -- the perception seems to be felt more by the passenger than the driver. The Pilot Sports are harsh and do tend to tramline.
If this is primarily your car and your wife only rides in it occasionally, then let her drive (if you can bear giving it up) when you travel together -- it's not worth giving up the AMG handling when you don't have her in the car. She'll have enough fun driving to forget about the ride quality (as above, the passenger effects are where it's really felt).
If that's not the case and you're really willing to surrender, then getting less aggressive tires, shocks and springs should work, but you're giving up a lot of $$ to de-ball your car.
'98 C43 AMG
'93 190E Limited Edition (including factory Sportline package)