Glad to hear you guys are getting some good results with this.
We asked a chemist, and he said that actually the disposal of the left over solution was simpler than we'd originally thought.
The copper salts (leftover sludge) were the thing that we were most concerned with. But he said that old copper pipes flake off small bits of copper all the time, so this small amount produced by a small etching setup wasn't a concern.
Just dilute the solution with plenty of water, and pour it down your drain or into your toilet.
Simple!