Yes you can. Here is a post where an owner of a SLK32 did just that.

This is a little tricky to explain as there are 2 coolant systems on the car with 1 common overflow container. Both systems use their own pumps but do not directly flow into one another. What I mean by this is that the water that cools the engine won't go into the intercooler system or vice versa. The only time the intercooler could get hot engine coolant is if the radiator puked some into the overflow (shared) container. If you car is running that hot then there is either something wrong or it is hotter then heck out.

There are still people separating the systems and here is the best example of that. This works great not because of the fact that he separated the systems from the common overflow but because he added a huge amount of coolant which the system really needed, especially in cases where people run more boost. The more coolant the less chance of heat soak & quicker recovery of lower air intake temps.