You will end up with the same issues.

Boiling isn't necessary. The particulate matter that flows through (poop, food, sand, other stuff, detritus) will accumulate in the rubble rock. The flow of water through the rubble rock will cause it to work loose and make it into your main tank.

My prediction is that the new rubble rock will build up a biological filtration and everything will be copecetic until the detritus builds up enough that it starts filtering into your main tank.

It's not your rubble rock set up that's giving you this, it's (and I'm assuming that you don't have one) the lack of a filter media to capture the detritus as it works its way back into the tank. And if you do have the filter media it should be replaced frequently to help pull that stuff from your system.