I think in this specific case, the options are either to fully define the indicator states in the stylesheet (if I understood the problem correctly), or to get down and dirty with the QItemDelegate for the QTreeView.
I played with that a bit, but have not found a good way to only change a color component. It is not actually a checkbox widget, but rather a paint style that draws it. You could draw your own checkbox however you want:
QItemDelegate.drawCheck()
You would subclass and implement drawCheck to paint the checkbox however you want. I know it sucks to have to do that much work. If it were actually a tangible QCheckBox widget, then you could just access it and set the palette.