Welcome Aboard.... I can't think of a single way to remove it with disrupting the entire system.... It'll still make some mess but since it's pretty shallow you could remove what you can by hand, using a gravel vaccum to remove as much of the crus as possible first, and cover the rest with sand. Presoaking the new sand in SW for a week or two will help reduce some of the sandstorm. If you dump it into the tank though it'll stir up for sure...best to try and get it to settle right to the bottom by using a hose and siphon it from another container into your tank.

Over time the CC will naurally rise to the top of the sandbed. The same way rocks grow in the garden, the finer particle sand will fill in below the CC and force it to the top. So just covering it all may not yield the results you want.