My first thought is "that's not meant to be done by this app".
Personally I would use a tool suited for that task (at the top of my head is ImageMagick).
Also, I would prefer to have the animations in a single spritesheet, in order to reduce the graphics card state changes, however, I'm not familiar with the Intersect Engine, so I don't know of that's an option.
That said, if none if these options work for you, I'll probably fit this change in the next release, no problem (the hide body is already done).