Could you put the pellets in the first chamber, getting the most flow/tumble and then since they would have canisters you can load up the 2nd (or add extra sponge if not using the entire tube) with carbon without causing much disruption?
Let me qualify that. Carbon needs slow flow in order for it to work. Its not a matter of tumbling or what not, but it needs slow contact time to adsorb whatever it is going to adsorb. Also carbon packed tight will slow the flow enough that it wont tumble the pellets properly and also clog much quicker especially with bacteria forming AFTER the pellet reactor.
Look into modding the reactor than you can control the flow separately. It only needs a few fittings.