Let's think about it here. In New Avengers#40 they showed at the end of the issue Spiderwoman being replaced by the Queen of Skrulls.
On the cover of Secret Invasion#3 show Spider-woman and Tony Stark kissing. Tony and Jessica have been working together on keeping this Skrull thing a secret? What if at towards the end of the saga they reveal Tony Stark is a skrull.