Update: Took a couple of days for the water to clear, but the fish seemed none the worse for wear. My filter stalled once, so I checked it religiously and it seems to be working just fine now. I went all sand and added pebbles on the surface in the corners of the tank, plus a bigger-rock "riverbed" through the center that goes under my cheesy little bridge. I like that I can see all the crap up top, and it's really very easy to clean at water changes, although getting the siphon stirs stuff up a bit.
Only problem now is that the sand gives the tank a little less color, so I'm going to need to add/chnage plants. So far I only have six pygmy cories and one dwarf gourami. Neons or cardinals are next, we'll see if they add a little color. I want to add a couple of ghost shrimp to help the cories clean up. I'd like a couple of guppies just to add a bit more color, but I have to be careful that I'm not overstocked (15G US).
Really am happy with the change, I like the natural look, and I like not worrying much about the corys, although they still do seem to enjoy picking around the pebbles.
Thanks again everyone for the advice.
Aaron