Didn't Wanda's "No More Mutants" spell have a multiverse effect? That's what the wiki said, don't know how true it is... but it would explain just how powerful she is. She is also connected to the Life Force and isn't that why she went crazy in the first place?
The Life Force could possibly be connected to the Phoenix Force which is why she is able to harm it and like someone else said, they are basically opposites, order and chaos.
I don't think they actually destroyed the Phoenix, it just split into many fragments and created more mutants. I also don't think that was the complete Phoenix either, the actual force is in many pieces which are being collected by Jean, right?