I'm currently following the elimination diet myself. I cook my fruit until soft, but not mushy. My understanding is that you just want to breakdown the proteins in the food a bit so they aren't so inflammatory.
On a side note, I've been using http://nutritiondata.self.com/
to monitor the Inflammation Factors of my food since starting the Elimination Diet. Then I came across the iPad app IF Tracker and started using it. I don't know how helpful either will be in the long run, but its more data for me (God! I am such a nerd!)