My own impression is this: that Ellen is still tremendously conflicted about her own creation because it was such a traumatic experience. She feels irrationally angry about it, which I fully understand. She had very conflicting feelings even about Tedd whom she until recently -- to be exact, this page -- held responsible for her creation because of his careless use of the TG gun and for his part in getting Elliot to the diamond. Now she has learned that Magus used Tedd, Elliot and her creation simply as tools to set himself free from his prison dimension. Acts born from desperation, yes -- but even understanding that, Ellen would still be furious, knowing as she now does that the sole reason for her existence is that she was intended as a one-shot zap device to give Magus the means of possessing Elliot. Granted, she has found meaning of her own since, but I really doubt that will calm her very much.
In short, she badly wants to give Magus a piece of her mind, and I do not really blame her.