Ah that is a dilemma! I'm not sure how to get around that in r12 unfortunately. I remember being able to do what you described before in r11, but we've had to make due with the new "As Tree" function in the reports.
Would it make sense to add slicers instead? That's what we've done to get around not being able to filter in the table itself. It obviously doesn't get you exactly what you envisioned, but should work to allow you to filter however you'd like.
Hope that helps!