http://en.wikipedia.org/wiki/Asajj_ventress
Reading her story before the Clone Wars cartoon, she seems to have been briefly a jedi apprentice. So her green and blue lightsabers make sense. That, and it also could be assumed that she got the lightsabers from some other jedi who was killed in the clone wars or she killed at some point. I wouldn't think one would need to recolor the sabers some other color.
But for your edit, I personally wouldn't be too concerned about keeping EU continutity with Ventress. Do what you want to do with it, and if it contradicts something in the EU, oh well. It seems like to me that they've pretty much turned Ventress into someone who is "just too cool to die" like Boba Fett.