Replacing with rock in the tower will not create a more efficient filter my friend. The trickle filter is extremely efficient already. The highly oxygenated media tower is designed for explosive bacterial growth.
Your understanding of nitrate is well, unclear I think.
Nitrate is a result of nutrient conversion. Fact is, the bio ball media houses bacteria which PRODUCE nitrate, not trap it. No trapping here; in fact the various crannies and cracks in the rock will likely trap more debris than your bio balls; which are designed not to trap anything. The rocks will quickly become covered/clogged with slime/detritus/gook. If the goal is to reduce the BACTERIA culture, you are simply replacing the balls with rock (more media) which will be replaced with more bacteria; maybe not as much bacteria but still will produce nitrate, so maybe not the best solution IMO. Before you go elminating or tinkering with your bio filter, please outline your complete system/filtration/bioload/current water parameters and any problems, then maybe I can offer more help. If, and again IF, you have a small bioload, enough live rock and a huge skimmer you may not need the bio media at all or maybe just reducing the balls will do the trick.
You also might need to research deep sand beds and tumbling macro algae filters as options for reducing nitrates.
