That is a brilliant idea. I've been using the filing system from the book "Organizing Your Family History Search" by Sharon DeBartolo Carmack.
I've been using a different color file folder for genealogy stuff. I think I will pull it all out into a separate drawer though as you are correct, it might get inadvertently thrown away if it's in the main filing system.
Color is helpful too - each of my file boxes is a separate color to allow for quick identification.
If I recall correctly, Carmack advises creating a file folder for every family group. This never worked for me because, ultimately, a person's data would be in at least 2 locations - the family group they were born into, and the family group they established upon marriage. Adding in files for locations or events that cover multiple families - this could get confusing!