The carbs in the psyllium husk do not get digested or assimilated, so even though it contains carbs it is okay on the diet.
Psyllium scrubs the intestinal walls and yes, so doing it will remove some good bacteria from the gut (especially so if you use it along with clay - P & B shakes) so supplementing after each intake is a good idea.
However, fiber (psyllium, flaxseed etc) is also a prebiotic. The traces that will get caught in intestinal pockets will then make a home for friendly bacteria.