Crimp the hose to control flow. Lighter poop goes up, sand goes back down.
The bacteria live ON the sand, the only ones you'll lose are attached to the bit of sand you will inevitably lose.
Arthropods (amphipods/copepods) will avoid the siphon too. If you think you're sucking them up, wait for your waste water to settle and try to see any. Chances are, you won't.
I always suggest putting rock on bare glass, then add sand. For one, you won't have an avalanche caused by a tunneling creature digging out the foundation from under the rocks, and crap won't get trapped in sand compressed by rocks. Yes, a bit of detritus will inevitably get there, cleaning substrate is not an exact science, but if you can get most of it out, that's a plus.
No matter how careful you are, you aren't going to get all of it. If you can get most of it, you're doing it right.
Jenn