As I understood the OP, this was not the question.
Perhaps in the next part of that, by "clear it" the OP means delete everything in it, but I didn't take it that way. However, "turning it off" is simple. Drag it off, which has the same effect as unchecking it in preferences. That does not delete the files. You can also just click the "disclosure triangle" and get the list to "roll up" and be out of sight.
But if OP means not having those things "tracked" in the Smart Folders, I'm not aware of a way to do that. I admit that I thought those were just aliases, and did not know you could delete the real file from that location. Good to know!
I also thought I'd read that these are not copies of the files, and thus do not take up more disk space. Maybe that led me to the above conclusion. So, is that not the case either?