I realize you're probably looking for some Photoshop and/or scanning advice, but I approached this problem from a different angle.
I found scanning inks with blue pencil underneath was always a drag for exactly the reasons you listed above. My solution was to scan my pencil work, color it blue or red in photoshop, and print out the REVERSE colored image on a piece of bristol.
Then I just inked over the reverse image face down on a light box. The finished inks were pristine for scanning and if a messed up, I could just print out another pencil scan.
I'm sure others could probably help out more with removing color and such, but I thought I'd throw that out there.