OK, I'll try making my dump one level lower than where the water is being pumped. Regarding Shade-o's suggestion about changing water level, I got my logs to be flushed when I stopped and restarted the pumps. My dumped stones, however, didn't move an inch.
Oh, and I didn't bother with this for practical reason, as my bottomless pit is close enough to my fort's main shaft that it would even make sense to dump shit directly in it.
Regarding atom-smashing, I think we've already talked about this. I'm not convinced about the realism of putting thousands of stones under a bridge and pulverizing them, though I guess hooking it up to a water-based repeater would make sense, so it would only smash small amounts of rock at a time.
Do you know of a way of avoiding phantom globs when magma-dumping rocks? I mean, would dumping stuff directly into the pipe be clean? Or what about pumping the magma dump around so the depth didn't remain constant?
EDIT:
1. Changing the z-level of where my water gets pumped didn't do anything. Any obsidian I've dumped, or am still dumping, won't move an inch.
2. Turns out, even the stuff that did get "flushed" didn't get disposed of properly. Looking at my stocks, I've seen a {withered pig tail} F that I had dumped earlier and thought had already disappeared down the bottomless pit. It's still being tracked in my stocks, and when I zoom in on it, I'm being shown its former location without it physically being there. This is fucking ridiculous.