I think a heavy does of chlorine will kill anything that might be growing in there. However, it does leave an organic residual that may allow future disease a foot hold and, as the roots breakdown, it could cause some congestion in your pipes.
All in all, I'd probably pull out the major visible root clumps and take my chances with what's left over. Since you're not relying on sprayers clogging shouldn't be an issue and since you didn't have "bugs" before, that shouldn't really be an issue either.
Just my feeling on it but, then, I am lazy.

I am trusting in the grizzman then :). Thanks for not saying I had to clean the stuff out.

When I replant, I am planning on flooding my ebb and flow system while I pull the plants out. I think this will make more of the root come with the plant.

H2O2 to disinfect is probably better than bleach (less residual I've been told).

Haven't tried it but there is a product, cannazyme, that claims to break down root matter into plant food.

Build a fire and cook the clay balls in a metal pot, barrel or bucket. It'll burn the roots to ash then just rinse it after the clay cools. It's already fired so shouldn't hurt it. But I've never dealt with clay balls. Have done this with crushed brick pieces though.