Are you going to bake this filling? I believe that it will weaken the starch, and possibly also the pectin to a lesser degree. Reheating it in order to incorporate more starch will weaken it as well. You might end up having to add quite a bit of starch.
I think that Jeanne's idea of draining the juice will be best.
Or you can make it into a crumble (or crisp, etc.) where a loose filling is welcome.