This is interesting to think about. As I'm sure you've considered, bacteria and other living cells exist in a state of highly regulated homeostasis. In bacteria, things like charged ion concentrations are maintained internally by various physiological mechanisms (chiefly the membrane-bound transport channels you describe) at specific concentrations with little variation. Salinity concentrations are generally the same as the surrounding seawater (marine bacteria are usually osmoconformers, as opposed to more sophisticated osmoregulators like fish), and the transport mechanisms exist as adaptations to maintain this state.

So while some aquatic bacteria can exist at a wide range of external salt concentrations (they are "euryhaline"), I don't know of any bacteria that have adaptated to actively concentrate salt internally above the salinity of typical seawater. Beyond a certain not-very-useful threshold, this would disrupt too many metabolic pathways and kill the bacterium. So I don't see how a concentrate-in-the-bacteria-then-filter-them-out approach to industrial desalination would work.

You might be thinking about brine pool extremophile bacteria / archaea, but again, they are just well-adapted when it comes to expelling salt or resisting salt intake, not actively concentrating it internally.

However, if you could embed euryhaline bacteria into some kind of impermeable membrane in a controlled orientation, and engineer them to express the right kind of one-way channels on opposite sides of the cell... there are some big bioengineering obstacles to doing this, but it's an interesting idea. It would basically be a sped-up version of the double reverse osmosis desalination approach already widely used, potentially more efficient and available to be powered more easily by sustainable / free energy sources.

I'm just typing as I think there, so maybe there's been work in this area already.