I'm actually willing to consider the idea that Wanda isn't responsible for that outside of being a pawn of forces outside of her control. The Life Entity for certain, but also Dr. Doom took responsibility for that attack, and it shows the kind of strategy that he would use moreso than the person Wanda is at her worst... and, ironically, ended in the sort of punishment that he swore he'd inflict on the Vision someday. It may well be his design at work.
My big problem with Doom being behind Wanda's problems is if Doom had control over a resource like Wanda...wouldn't he have made a point to spread some of that misery onto the Fantastic Four instead of inflicting it on the Avengers and the mutants?
Doom using Wanda means he effectively used her to commit mass genocide (even though he's not racist/specist IMO) and dismantled the Avengers. He couldn't share the hate with his worst enemies? Doom dismantled the Avengers, had mutants wiped out and still he had lame fights with the Fantastic Four. Making Doom behind Wanda's problems makes it seem like he's kind of...well...outgrown the Fantastic Four.
I assume Doom didn't have fine control... he could only direct Wanda subtly, and in ways that her own darker side and subconscious fears had considered. Wanda simply doesn't think enough about the FF for her to be directed in that way. Although that's TOTALLY why he'd have had her kill Agatha by cancelling her resurrection... spite the FF in that way, by killing Franklin's nanny, and HOPE that the chaos caused in New York in Disassembled might accidentally pick off some of the FF. Either way, Richards' allies are downed, and Doom wins that way. (The What If?, of course, says that the strategist Wanda was using was Captain America, who was slowly going senile... a thing that that world's Dr. Strange confirmed was true of the 616 Universe as well, so there's that little tidbit to factor.)
I also think that the "No More Mutants" thing was one of those plans that totally went outside of Doom's control. He didn't expect Wanda's hate of her father to end up that way, and his subtle influence, intended to eliminate the only man he views as a genuine rival for control of the world (as was established in Super-Villain Team-Up), sort of spiraled into that.