At the beginning of the movie, Peter tells Miles he cannot trusted anyone
When Kingpin unmasks Peter, he isn't surprised in the slightest at his identity
At no point in the film is MJ involved with the heroes
MJ herself is perfectly calm at Kingpin's party
MJ speaks at Kingpin's party and is not visibly distressed at all being near the murderer of her husband
At no point is any effort made to include MJ in the plan to stop Kingpin, even though it is clearly established that she has an in with Kingpin
Conclusion: MJ most likely betrayed Peter to Kingpin, and this is why her presence is mostly glossed over. She's one of the bad guys.