A simple solution, which I've been using for ages now, is opening a command prompt yourself and running the executable manually. An advantage of this method is that you can set your "DOS" window's size to anything you want. (Right now I'm using a 120x50 window with 8192 lines of scrollback buffer.) Another one is that you will never lose your console output; in fact, you'll be able to see outputs from past runs. (8192 lines is A LOT unless you're printf-debugging a tight loop.)
An alternative to terminating your program from the taskbar is using the red icons on the top right corner of the Eclipse "Console" window.