A product called
remote key.
Wilhelmy-IT Inc. smartTOP - remoteTOP - remoteKEY Porsche Carrera Boxster Mercedes Benz SLK SL CLK Comfort One-Touch Soft-Top roof control units and Comfort remote controllers
There are whole threads on this product that you can search for on the forum. Bottom line is the product adds tons of functionality. Windows up/down is one of like 7 or 8 features you can choose to enable or disable once the box is installed.
It does take a few minutes to install, and requires a bit of skill, but nothing that someone couldn't do themselves.
I have had one installed since day one, and I haven't looked back.
Good luck.