If one of the main reasons for having the refuge was to provide food for a specialized feeder such as a mandarin or perhaps your corals then your definitely compromising this by running the sock IMO. What goes up must come down and vice versa. It's not like the pods can dodge the sock or anything. Like mentioned above though using one probably won't destroy the micro fauna population, but your definitely putting a dent in it.
As far as keeping your sump clean goes, it's real easy to make a vacuum with certain power heads and some vinyl tubing. Lots of hobbyists here at RC do this. GL.