Changing colours is laborious. One option would be to allow multiple settings to be defined by the user (Zenburn, Solarised, My Really Neat Yellow on Pink, etc...) and then select one from a dropdown.
A simpler but uglier way would be to allow programs to rewrite console.xml and then force a running Console instance to reload it. Then I could write my own script to manage the colours. At the moment, a program that edits console.xml can only be run while console is not running.