I have a different solution to this that works for my situation, and can probably be adapted by others.
I actually want a real second console window -- gnome-terminal in my case. I want this because I want ANSI color support and I want JLine to operate correctly. I can separately start my program and connect remotely for debugging, but that's annoying.
Locate where Java runs from, for the JRE eclipse will run as part of your debug config. Create a script there named gjava, give it the following content, and set it executable:
#!/bin/sh
gnome-terminal -x java $*
Then, in your launch configuration, on the common page, uncheck "Allocate console". On the JRE page, under Java executable, choose "Alternate" and enter gjava.
When Eclipse launches in debug mode, it will launch a gnome terminal and pass the remaining args to the Java processor, which will be running inside its window.
At that point you have a real console that supports JLine, ANSI colors, and full debug support.