EXACTLY. Anyone who says they are cleaning your cistern , and DOES NOT first empty all of the water, and then scrub down the walls, get rid of all sediment/debris on the floor, scrub the floor and rinse it, then rinse the walls and floor with Clorox, rinse that down with lots of clean water, and then pump that out, and then finally refill the cistern, has just ripped you off. That's the way to clean a cistern.
During this process, also make sure that someone is outside and watching the guy inside while cleaning, as the Clorox fumes can become quite strong, and they can help if the guy inside should be affected.(right - Breathing apparatus - here??)
Just remember to not restart the pump until the intake pipe to the pump (that's probably a 1 1/2" or 2" pipe comind down the cistern wall with an open end facing the floor, and ending about 18" above the floor of you now-clean cistern) is at least 6" below the water's surface, or you will be running the pump while it's dry, and destroy the pump in the process).
What good does it do, to do it any other way? All of the crud in the cistern doesn't go anywhere except into your water pipes.
This should be done at least once a year, if not twice. Also should be done if it rains and floods, and any water enters your cistern from outside. Immediately.